Diabetes
The Gene Signature Commons Group
2020-10-20
Source: https://github.com/markziemann/gene_sig_commons
Background
This analysis is an example of how gene signatures can be generated from publicly available omics data. In this example, we will obtain data from the DEE2 database, perform differential analysis with DESeq2 and then return the gene signature.
source("../de_functions.R")# let's assume species is human for now
SPECIES = "hsapiens"
# read in the file
x <- readLines("../contrasts/diabetes.md")
# this is the best way to get studies with contrasts set up
x <- x[grep("RP",x)]
# how many contrasts to do?
length(x)## [1] 114# get the metadata now to save time
mdat <- getDEE2::getDEE2Metadata(species = SPECIES)
# lets prototype this: main(x[[2]],mdat)
# now go ahead and run the whole thing
data <- lapply(x,function(x) { main(x,mdat) })## SRP221142:Genes differentially regulated by pro-inflammatory cytokines:Ctrl; SRX6821381,SRX6821383,SRX6821385,SRX6821387,SRX6821389:PIC; SRX6821382,SRX6821384,SRX6821386,SRX6821388,SRX6821390## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR10088643: int [1:58302] 3 335 28 3 0 0 3 0 0 1 ...
## ..$ SRR10088644: int [1:58302] 0 144 17 0 0 0 2 0 0 2 ...
## ..$ SRR10088645: int [1:58302] 0 271 18 2 0 0 5 1 0 3 ...
## ..$ SRR10088646: int [1:58302] 0 343 23 1 0 0 10 0 0 2 ...
## ..$ SRR10088647: int [1:58302] 3 128 11 1 0 0 1 0 0 2 ...
## ..$ SRR10088648: int [1:58302] 2 365 51 4 0 0 0 0 0 1 ...
## ..$ SRR10088649: int [1:58302] 1 280 14 3 0 0 0 0 0 2 ...
## ..$ SRR10088650: int [1:58302] 0 305 24 1 0 2 4 0 0 0 ...
## ..$ SRR10088651: int [1:58302] 3 442 24 2 0 0 0 0 0 1 ...
## ..$ SRR10088652: int [1:58302] 1 383 26 3 0 0 1 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR10088643: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10088644: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10088645: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10088646: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10088647: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10088648: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10088649: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10088650: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10088651: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10088652: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR10088643: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR10088644: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR10088645: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR10088646: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR10088647: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR10088648: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR10088649: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR10088650: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR10088651: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR10088652: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:10] "SRX6821381" "SRX6821382" "SRX6821383" "SRX6821384" ...
## ..$ SRS_accession: chr [1:10] "SRS5363958" "SRS5363959" "SRS5363960" "SRS5363961" ...
## ..$ SRP_accession: chr [1:10] "SRP221142" "SRP221142" "SRP221142" "SRP221142" ...
## ..$ Sample_name : chr [1:10] "GSM4067526" "GSM4067527" "GSM4067528" "GSM4067529" ...
## ..$ GEO_series : chr [1:10] "GSE137136" "GSE137136" "GSE137136" "GSE137136" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:10] "SRX6821381" "SRX6821382" "SRX6821383" "SRX6821384" ...
## ..$ SRS_accession : chr [1:10] "SRS5363958" "SRS5363959" "SRS5363960" "SRS5363961" ...
## ..$ SRP_accession : chr [1:10] "SRP221142" "SRP221142" "SRP221142" "SRP221142" ...
## ..$ Sample_name : chr [1:10] "GSM4067526" "GSM4067527" "GSM4067528" "GSM4067529" ...
## ..$ GEO_series : chr [1:10] "GSE137136" "GSE137136" "GSE137136" "GSE137136" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM4067526" "GSM4067527" "GSM4067528" "GSM4067529" ...
## ..$ ReleaseDate : chr [1:10] "2019-09-20 16:07:39" "2019-09-20 16:07:39" "2019-09-20 16:07:39" "2019-09-20 16:07:39" ...
## ..$ LoadDate : chr [1:10] "2019-09-09 18:36:18" "2019-09-09 17:50:42" "2019-09-09 17:56:00" "2019-09-09 18:04:08" ...
## ..$ spots : int [1:10] 119898489 54472778 85122073 114821406 60891015 116000000 72665319 85320664 118787727 90312380
## ..$ bases : num [1:10] 2.42e+10 1.10e+10 1.72e+10 2.32e+10 1.23e+10 ...
## ..$ spots_with_mates : int [1:10] 119898489 54472778 85122073 114821406 60891015 116000000 72665319 85320664 118787727 90312380
## ..$ avgLength : int [1:10] 202 202 202 202 202 202 202 202 202 202
## ..$ size_MB : int [1:10] 17736 8138 12413 16713 8830 16830 9333 10928 16098 12228
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra78/SRR/009852/SRR10088643" "https://sra-download.ncbi.nlm.nih.gov/traces/sra71/SRR/009852/SRR10088644" "https://sra-download.ncbi.nlm.nih.gov/traces/sra78/SRR/009852/SRR10088645" "https://sra-download.ncbi.nlm.nih.gov/traces/sra78/SRR/009852/SRR10088646" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:10] "SRP221142" "SRP221142" "SRP221142" "SRP221142" ...
## ..$ BioProject : chr [1:10] "PRJNA564614" "PRJNA564614" "PRJNA564614" "PRJNA564614" ...
## ..$ Study_Pubmed_id : logi [1:10] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:10] 564614 564614 564614 564614 564614 564614 564614 564614 564614 564614
## ..$ Sample : chr [1:10] "SRS5363958" "SRS5363959" "SRS5363960" "SRS5363961" ...
## ..$ BioSample : chr [1:10] "SAMN12718008" "SAMN12718007" "SAMN12718006" "SAMN12718005" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA958993" "SRA958993" "SRA958993" "SRA958993" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "E0BCDFF87AAB7BAEA59B9F907C237BC8" "A50FAC06690E5B494BE9551D7643B984" "473BB794894549C7D3362D29B94E4641" "A57C2ACE1B79211B1EF584275D0832F5" ...
## ..$ ReadHash : chr [1:10] "46E8B8C0063766F6C55DC0292985725B" "B2CEB9A26C261BAAC73F6122330EC1B8" "D66B1EB4FCBDBF9FCA98ED5851D2A8C4" "A509DE4EE14FE10C954B5381AC352867" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP032953:Down regulation of miRNA contributing to T2DM:Ctrl; SRX376828,SRX376829,SRX376830:T2DM;SRX376831,SRX376832,SRX376833,SRX376834## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR1028929: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1028930: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1028932: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1028933: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1028934: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1028935: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1028929: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1028930: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1028932: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1028933: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1028934: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1028935: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR1028929: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR1028930: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR1028932: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR1028933: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR1028934: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR1028935: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,6,7)" ...
## ..$ SRX_accession: chr [1:6] "SRX376828" "SRX376829" "SRX376831" "SRX376832" ...
## ..$ SRS_accession: chr [1:6] "SRS502225" "SRS502226" "SRS502229" "SRS502231" ...
## ..$ SRP_accession: chr [1:6] "SRP032953" "SRP032953" "SRP032953" "SRP032953" ...
## ..$ Sample_name : chr [1:6] "GSM1262775" "GSM1262776" "GSM1262778" "GSM1262779" ...
## ..$ GEO_series : chr [1:6] "GSE52314" "GSE52314" "GSE52314" "GSE52314" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,6,7)" ...
## ..$ SRX_accession : chr [1:6] "SRX376828" "SRX376829" "SRX376831" "SRX376832" ...
## ..$ SRS_accession : chr [1:6] "SRS502225" "SRS502226" "SRS502229" "SRS502231" ...
## ..$ SRP_accession : chr [1:6] "SRP032953" "SRP032953" "SRP032953" "SRP032953" ...
## ..$ Sample_name : chr [1:6] "GSM1262775" "GSM1262776" "GSM1262778" "GSM1262779" ...
## ..$ GEO_series : chr [1:6] "GSE52314" "GSE52314" "GSE52314" "GSE52314" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1262775" "GSM1262776" "GSM1262778" "GSM1262779" ...
## ..$ ReleaseDate : chr [1:6] "2013-12-02 09:57:07" "2015-07-22 17:04:09" "2013-12-02 09:57:07" "2013-12-02 09:57:07" ...
## ..$ LoadDate : chr [1:6] "2013-11-12 18:18:42" "2015-12-09 20:33:52" "2013-11-12 18:19:01" "2013-11-12 18:19:03" ...
## ..$ spots : int [1:6] 2039741 3789588 4546604 5833440 11280601 11660182
## ..$ bases : int [1:6] 73430676 136425168 163677744 210003840 406101636 419766552
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 36 36 36 36 36 36
## ..$ size_MB : int [1:6] 65 105 136 116 302 314
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1028929/SRR1028929.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1028930/SRR1028930.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1028932/SRR1028932.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1028933/SRR1028933.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" ...
## ..$ SRAStudy : chr [1:6] "SRP032953" "SRP032953" "SRP032953" "SRP032953" ...
## ..$ BioProject : chr [1:6] "PRJNA227380" "PRJNA227380" "PRJNA227380" "PRJNA227380" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 227380 227380 227380 227380 227380 227380
## ..$ Sample : chr [1:6] "SRS502225" "SRS502226" "SRS502229" "SRS502231" ...
## ..$ BioSample : chr [1:6] "SAMN02401881" "SAMN02401879" "SAMN02401884" "SAMN02401883" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA111063" "SRA111063" "SRA111063" "SRA111063" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "40BAC8ED729F835795C422D5F1E466A4" "F89D66C83C661F5988F184D7EEB2CECA" "C25B68FDDD73FBFA8FF94D33DDC36CE9" "A6EF92EAD298DFE391092FD16CA53160" ...
## ..$ ReadHash : chr [1:6] "AB9E8C0A4FD83BED444A9F6FD630FA99" "36376D509B215A591079B9AFB657A019" "3E3D0E801C71A33D5E7B70C7D6E15A24" "0BC36FFCF36EECB399CED972E5EC3657" ...
## $ absent : chr(0)## SRP228577:Genes differentially regulated by insulin induction and APBBR treatment:Ctrl; SRX7100386,SRX7100387,SRX7100388:APBBR; SRX7100383,SRX7100384,SRX7100385
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR10400224: int [1:58302] 0 167 2 0 0 0 0 0 0 0 ...
## ..$ SRR10400225: int [1:58302] 0 133 6 0 0 0 0 0 0 0 ...
## ..$ SRR10400226: int [1:58302] 0 114 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400227: int [1:58302] 0 204 2 1 0 0 0 0 0 0 ...
## ..$ SRR10400228: int [1:58302] 0 124 2 0 0 0 0 0 0 0 ...
## ..$ SRR10400229: int [1:58302] 0 214 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR10400224: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400225: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400226: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400227: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400228: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400229: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR10400224: chr [1:30] "PE" "Sanger/Illumina1.9" "102" "151" ...
## ..$ SRR10400225: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "151" ...
## ..$ SRR10400226: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "151" ...
## ..$ SRR10400227: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "151" ...
## ..$ SRR10400228: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "151" ...
## ..$ SRR10400229: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "151" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(4,6)" "FAIL(4)" ...
## ..$ SRX_accession: chr [1:6] "SRX7100383" "SRX7100384" "SRX7100385" "SRX7100386" ...
## ..$ SRS_accession: chr [1:6] "SRS5612645" "SRS5612646" "SRS5612647" "SRS5612648" ...
## ..$ SRP_accession: chr [1:6] "SRP228577" "SRP228577" "SRP228577" "SRP228577" ...
## ..$ Sample_name : chr [1:6] "GSM4149705" "GSM4149706" "GSM4149707" "GSM4149708" ...
## ..$ GEO_series : chr [1:6] "GSE139929" "GSE139929" "GSE139929" "GSE139929" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(4,6)" "FAIL(4)" ...
## ..$ SRX_accession : chr [1:6] "SRX7100383" "SRX7100384" "SRX7100385" "SRX7100386" ...
## ..$ SRS_accession : chr [1:6] "SRS5612645" "SRS5612646" "SRS5612647" "SRS5612648" ...
## ..$ SRP_accession : chr [1:6] "SRP228577" "SRP228577" "SRP228577" "SRP228577" ...
## ..$ Sample_name : chr [1:6] "GSM4149705" "GSM4149706" "GSM4149707" "GSM4149708" ...
## ..$ GEO_series : chr [1:6] "GSE139929" "GSE139929" "GSE139929" "GSE139929" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4149705" "GSM4149706" "GSM4149707" "GSM4149708" ...
## ..$ ReleaseDate : chr [1:6] "2019-11-21 00:59:20" "2019-11-21 00:59:20" "2019-11-21 00:59:20" "2019-11-21 00:59:20" ...
## ..$ LoadDate : chr [1:6] "2019-11-06 08:50:38" "2019-11-06 08:46:25" "2019-11-06 08:37:06" "2019-11-06 08:42:44" ...
## ..$ spots : int [1:6] 53330386 49090729 43207188 42234834 44359110 45869893
## ..$ bases : num [1:6] 1.60e+10 1.47e+10 1.30e+10 1.27e+10 1.32e+10 ...
## ..$ spots_with_mates : int [1:6] 53330386 49090729 43207188 42234834 44359110 45869893
## ..$ avgLength : int [1:6] 299 299 300 300 298 299
## ..$ size_MB : int [1:6] 5933 5319 4791 4703 4797 5044
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra29/SRR/010156/SRR10400224" "https://sra-download.ncbi.nlm.nih.gov/traces/sra2/SRR/010156/SRR10400225" "https://sra-download.ncbi.nlm.nih.gov/traces/sra15/SRR/010156/SRR10400226" "https://sra-download.ncbi.nlm.nih.gov/traces/sra73/SRR/010156/SRR10400227" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:6] "SRP228577" "SRP228577" "SRP228577" "SRP228577" ...
## ..$ BioProject : chr [1:6] "PRJNA587640" "PRJNA587640" "PRJNA587640" "PRJNA587640" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 587640 587640 587640 587640 587640 587640
## ..$ Sample : chr [1:6] "SRS5612645" "SRS5612646" "SRS5612647" "SRS5612648" ...
## ..$ BioSample : chr [1:6] "SAMN13197979" "SAMN13197978" "SAMN13197977" "SAMN13197976" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA991467" "SRA991467" "SRA991467" "SRA991467" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "44D8527181446EE2F9C89BBFA9D3F748" "890CAE7CECDEF567D4F470648337A0D1" "0D2907C954D45DF1B9FC037E8FEB7C91" "FBA6A3CA812E58CFC7BCCEB80E2B77C7" ...
## ..$ ReadHash : chr [1:6] "69BF4FF14E716CBB0DCBFD9CBFCDA441" "E8CC8C15275C92573FE4F8A1A26A0F4E" "A52AFC6EAE6625177375BC2EB0BB6D37" "6264D313E78961DAA6CF8DF6237C9928" ...
## $ absent : chr(0)## SRP228577:Genes differentially regulated by insulin induction:Ctrl; SRX7100386,SRX7100387,SRX7100388:II; SRX7100389,SRX7100390,SRX7100391
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR10400227: int [1:58302] 0 204 2 1 0 0 0 0 0 0 ...
## ..$ SRR10400228: int [1:58302] 0 124 2 0 0 0 0 0 0 0 ...
## ..$ SRR10400229: int [1:58302] 0 214 1 0 0 0 0 0 0 0 ...
## ..$ SRR10400230: int [1:58302] 0 142 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400231: int [1:58302] 0 137 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400232: int [1:58302] 0 124 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR10400227: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400228: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400229: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400230: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400231: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10400232: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR10400227: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "151" ...
## ..$ SRR10400228: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "151" ...
## ..$ SRR10400229: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "151" ...
## ..$ SRR10400230: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "151" ...
## ..$ SRR10400231: chr [1:30] "PE" "Sanger/Illumina1.9" "104" "151" ...
## ..$ SRR10400232: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "151" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(4)" "WARN(3,4,6)" "WARN(3,4,6)" "FAIL(4)" ...
## ..$ SRX_accession: chr [1:6] "SRX7100386" "SRX7100387" "SRX7100388" "SRX7100389" ...
## ..$ SRS_accession: chr [1:6] "SRS5612648" "SRS5612649" "SRS5612650" "SRS5612651" ...
## ..$ SRP_accession: chr [1:6] "SRP228577" "SRP228577" "SRP228577" "SRP228577" ...
## ..$ Sample_name : chr [1:6] "GSM4149708" "GSM4149709" "GSM4149710" "GSM4149711" ...
## ..$ GEO_series : chr [1:6] "GSE139929" "GSE139929" "GSE139929" "GSE139929" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "FAIL(4)" "WARN(3,4,6)" "WARN(3,4,6)" "FAIL(4)" ...
## ..$ SRX_accession : chr [1:6] "SRX7100386" "SRX7100387" "SRX7100388" "SRX7100389" ...
## ..$ SRS_accession : chr [1:6] "SRS5612648" "SRS5612649" "SRS5612650" "SRS5612651" ...
## ..$ SRP_accession : chr [1:6] "SRP228577" "SRP228577" "SRP228577" "SRP228577" ...
## ..$ Sample_name : chr [1:6] "GSM4149708" "GSM4149709" "GSM4149710" "GSM4149711" ...
## ..$ GEO_series : chr [1:6] "GSE139929" "GSE139929" "GSE139929" "GSE139929" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4149708" "GSM4149709" "GSM4149710" "GSM4149711" ...
## ..$ ReleaseDate : chr [1:6] "2019-11-21 00:59:20" "2019-11-21 00:59:20" "2019-11-21 00:59:20" "2019-11-21 00:59:20" ...
## ..$ LoadDate : chr [1:6] "2019-11-06 08:42:44" "2019-11-06 08:43:09" "2019-11-06 08:44:25" "2019-11-06 08:44:11" ...
## ..$ spots : int [1:6] 42234834 44359110 45869893 46183067 43828252 45799324
## ..$ bases : num [1:6] 1.27e+10 1.32e+10 1.38e+10 1.38e+10 1.32e+10 ...
## ..$ spots_with_mates : int [1:6] 42234834 44359110 45869893 46183067 43828252 45799324
## ..$ avgLength : int [1:6] 300 298 299 299 300 299
## ..$ size_MB : int [1:6] 4703 4797 5044 5047 4884 4995
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra73/SRR/010156/SRR10400227" "https://sra-download.ncbi.nlm.nih.gov/traces/sra38/SRR/010156/SRR10400228" "https://sra-download.ncbi.nlm.nih.gov/traces/sra29/SRR/010156/SRR10400229" "https://sra-download.ncbi.nlm.nih.gov/traces/sra41/SRR/010156/SRR10400230" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:6] "SRP228577" "SRP228577" "SRP228577" "SRP228577" ...
## ..$ BioProject : chr [1:6] "PRJNA587640" "PRJNA587640" "PRJNA587640" "PRJNA587640" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 587640 587640 587640 587640 587640 587640
## ..$ Sample : chr [1:6] "SRS5612648" "SRS5612649" "SRS5612650" "SRS5612651" ...
## ..$ BioSample : chr [1:6] "SAMN13197976" "SAMN13197975" "SAMN13197974" "SAMN13197973" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA991467" "SRA991467" "SRA991467" "SRA991467" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "FBA6A3CA812E58CFC7BCCEB80E2B77C7" "7E50B74D33A145F41730BFE3A1A243BA" "CBAFB26FFD3590301F1C7B0AE8437515" "AB1C6C4B239B18A8507472452BA22A39" ...
## ..$ ReadHash : chr [1:6] "6264D313E78961DAA6CF8DF6237C9928" "F8805F41405DC9BEC1BF8D146DCEDD98" "E2F7F15EC02B0ED21EF193B0EA9ED5A3" "BFA2CDC4446A349E13A523028B4AB164" ...
## $ absent : chr(0)## SRP233503:Genes differentially regulated by free fatty acids in HUVECs cells:Ctrl; SRX7228895,SRX7228896,SRX7228897:FFA; SRX7228898,SRX7228899,SRX7228900;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR10546621: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10546623: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR10546624: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR10546625: int [1:58302] 0 9 1 0 0 0 0 0 0 0 ...
## ..$ SRR10546626: int [1:58302] 0 5 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR10546621: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10546623: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10546624: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10546625: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10546626: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR10546621: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR10546623: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR10546624: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR10546625: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR10546626: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "WARN(4,8)" "WARN(4,6,8)" "WARN(4,6,8)" "WARN(4,6,8)" ...
## ..$ SRX_accession: chr [1:5] "SRX7228895" "SRX7228897" "SRX7228898" "SRX7228899" ...
## ..$ SRS_accession: chr [1:5] "SRS5729620" "SRS5729622" "SRS5729623" "SRS5729624" ...
## ..$ SRP_accession: chr [1:5] "SRP233503" "SRP233503" "SRP233503" "SRP233503" ...
## ..$ Sample_name : chr [1:5] "GSM4195641" "GSM4195643" "GSM4195644" "GSM4195645" ...
## ..$ GEO_series : chr [1:5] "GSE141126" "GSE141126" "GSE141126" "GSE141126" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "WARN(4,8)" "WARN(4,6,8)" "WARN(4,6,8)" "WARN(4,6,8)" ...
## ..$ SRX_accession : chr [1:5] "SRX7228895" "SRX7228897" "SRX7228898" "SRX7228899" ...
## ..$ SRS_accession : chr [1:5] "SRS5729620" "SRS5729622" "SRS5729623" "SRS5729624" ...
## ..$ SRP_accession : chr [1:5] "SRP233503" "SRP233503" "SRP233503" "SRP233503" ...
## ..$ Sample_name : chr [1:5] "GSM4195641" "GSM4195643" "GSM4195644" "GSM4195645" ...
## ..$ GEO_series : chr [1:5] "GSE141126" "GSE141126" "GSE141126" "GSE141126" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM4195641" "GSM4195643" "GSM4195644" "GSM4195645" ...
## ..$ ReleaseDate : chr [1:5] "2019-12-22 11:59:13" "2019-12-22 11:59:13" "2019-12-22 11:59:13" "2019-12-22 11:59:13" ...
## ..$ LoadDate : chr [1:5] "2019-11-27 23:21:31" "2019-11-27 23:21:25" "2019-11-27 23:23:50" "2019-11-27 23:22:21" ...
## ..$ spots : int [1:5] 29924662 30125617 41521923 33459969 41375823
## ..$ bases : num [1:5] 5.98e+09 6.03e+09 8.30e+09 6.69e+09 8.28e+09
## ..$ spots_with_mates : int [1:5] 29924662 30125617 41521923 33459969 41375823
## ..$ avgLength : int [1:5] 200 200 200 200 200
## ..$ size_MB : int [1:5] 4002 4025 5557 4457 5539
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-download.ncbi.nlm.nih.gov/traces/sra10/SRR/010299/SRR10546621" "https://sra-download.ncbi.nlm.nih.gov/traces/sra4/SRR/010299/SRR10546623" "https://sra-download.ncbi.nlm.nih.gov/traces/sra20/SRR/010299/SRR10546624" "https://sra-download.ncbi.nlm.nih.gov/traces/sra37/SRR/010299/SRR10546625" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:5] "SRP233503" "SRP233503" "SRP233503" "SRP233503" ...
## ..$ BioProject : chr [1:5] "PRJNA592178" "PRJNA592178" "PRJNA592178" "PRJNA592178" ...
## ..$ Study_Pubmed_id : int [1:5] 3 3 3 3 3
## ..$ ProjectID : int [1:5] 592178 592178 592178 592178 592178
## ..$ Sample : chr [1:5] "SRS5729620" "SRS5729622" "SRS5729623" "SRS5729624" ...
## ..$ BioSample : chr [1:5] "SAMN13413452" "SAMN13413459" "SAMN13413458" "SAMN13413457" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA1003767" "SRA1003767" "SRA1003767" "SRA1003767" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "FBE74D9B1AF16DCECEC84DC91890B82B" "6B1FA5B92A67CA935A96F912CC1E3112" "C51ED5A6285820EDDAF59AA4C578B6F2" "F16DACC3CBE3463BD40E118F726CF983" ...
## ..$ ReadHash : chr [1:5] "96E1CFAB98E130667E932B114D83A78C" "3978FE8B974A24F1D498693D131A6585" "A39C02B5790141CBA1C8BC73907B166F" "24AEACAF2B70188B9040197B7B1429EB" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP239527:Genes expressed differenially in unstimulated healthy donor cells vs unstimulated type 1 diabetes cells:HDOunstim; SRX7503269,SRX7503270,SRX7503271,SRX7503272,SRX7503273:T1Dunstim; SRX7503284,SRX7503285,SRX7503286,SRX7503287,SRX7503288## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR10829901: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829902: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829903: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829904: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829905: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829916: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829917: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829918: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829919: int [1:58302] 1 3 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829920: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR10829901: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829902: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829903: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829904: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829905: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829916: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829917: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829918: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829919: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829920: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR10829901: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829902: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829903: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829904: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829905: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829916: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829917: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829918: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829919: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829920: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX7503269" "SRX7503270" "SRX7503271" "SRX7503272" ...
## ..$ SRS_accession: chr [1:10] "SRS5944437" "SRS5944438" "SRS5944439" "SRS5944440" ...
## ..$ SRP_accession: chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250898" "GSM4250899" "GSM4250900" "GSM4250901" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX7503269" "SRX7503270" "SRX7503271" "SRX7503272" ...
## ..$ SRS_accession : chr [1:10] "SRS5944437" "SRS5944438" "SRS5944439" "SRS5944440" ...
## ..$ SRP_accession : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250898" "GSM4250899" "GSM4250900" "GSM4250901" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM4250898" "GSM4250899" "GSM4250900" "GSM4250901" ...
## ..$ ReleaseDate : chr [1:10] "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" ...
## ..$ LoadDate : chr [1:10] "2020-01-06 10:18:54" "2020-01-06 10:18:08" "2020-01-06 10:19:25" "2020-01-06 10:18:27" ...
## ..$ spots : int [1:10] 20717200 20108918 22853719 21389517 18892230 24557483 21599113 22707477 21757324 20717072
## ..$ bases : int [1:10] 1056577200 1025554818 1165539669 1090865367 963503730 1252431633 1101554763 1158081327 1109623524 1056570672
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 51 51 51 51 51 51 51 51 51 51
## ..$ size_MB : int [1:10] 385 370 419 391 348 449 400 421 401 383
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra7/SRR/010576/SRR10829901" "https://sra-download.ncbi.nlm.nih.gov/traces/sra51/SRR/010576/SRR10829902" "https://sra-download.ncbi.nlm.nih.gov/traces/sra70/SRR/010576/SRR10829903" "https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/010576/SRR10829904" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ BioProject : chr [1:10] "PRJNA599088" "PRJNA599088" "PRJNA599088" "PRJNA599088" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 599088 599088 599088 599088 599088 599088 599088 599088 599088 599088
## ..$ Sample : chr [1:10] "SRS5944437" "SRS5944438" "SRS5944439" "SRS5944440" ...
## ..$ BioSample : chr [1:10] "SAMN13738743" "SAMN13738742" "SAMN13738741" "SAMN13738740" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA1020255" "SRA1020255" "SRA1020255" "SRA1020255" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "55BF35373F0257351F0D34C4007B700C" "34ECE45C65E30A81FB49819DA53B7E4F" "A465C6ED4F49CAF25918ECEEA65A3C6F" "7D64256D57958B60FA44F9F018BD303A" ...
## ..$ ReadHash : chr [1:10] "1D9C667121E313B1D4EB6825A7A083C4" "6FF36B70172D786BC1495AFDD4746FA0" "378AA2B084F112D38EF3AD7C15B4B86B" "6269C7E34EDD7660EAAC7C1CEB860FAC" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP239527:Genes expressed differenially in unstimulated healthy donor cells vs type 1 diabetes cells stimulated by Neutrophil extracellular traps from healthy donor cells:HDOunstim; SRX7503269,SRX7503270,SRX7503271,SRX7503272,SRX7503273:T1D+HDONET;SRX7503289,SRX7503290,SRX7503291,SRX7503292,SRX7503293## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR10829901: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829902: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829903: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829904: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829905: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829921: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829922: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829923: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829924: int [1:58302] 0 3 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829925: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR10829901: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829902: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829903: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829904: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829905: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829921: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829922: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829923: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829924: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829925: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR10829901: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829902: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829903: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829904: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829905: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829921: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829922: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829923: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829924: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829925: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX7503269" "SRX7503270" "SRX7503271" "SRX7503272" ...
## ..$ SRS_accession: chr [1:10] "SRS5944437" "SRS5944438" "SRS5944439" "SRS5944440" ...
## ..$ SRP_accession: chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250898" "GSM4250899" "GSM4250900" "GSM4250901" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX7503269" "SRX7503270" "SRX7503271" "SRX7503272" ...
## ..$ SRS_accession : chr [1:10] "SRS5944437" "SRS5944438" "SRS5944439" "SRS5944440" ...
## ..$ SRP_accession : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250898" "GSM4250899" "GSM4250900" "GSM4250901" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM4250898" "GSM4250899" "GSM4250900" "GSM4250901" ...
## ..$ ReleaseDate : chr [1:10] "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" ...
## ..$ LoadDate : chr [1:10] "2020-01-06 10:18:54" "2020-01-06 10:18:08" "2020-01-06 10:19:25" "2020-01-06 10:18:27" ...
## ..$ spots : int [1:10] 20717200 20108918 22853719 21389517 18892230 18882937 23378418 24869341 19961170 18552981
## ..$ bases : int [1:10] 1056577200 1025554818 1165539669 1090865367 963503730 963029787 1192299318 1268336391 1018019670 946202031
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 51 51 51 51 51 51 51 51 51 51
## ..$ size_MB : int [1:10] 385 370 419 391 348 348 432 460 368 344
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra7/SRR/010576/SRR10829901" "https://sra-download.ncbi.nlm.nih.gov/traces/sra51/SRR/010576/SRR10829902" "https://sra-download.ncbi.nlm.nih.gov/traces/sra70/SRR/010576/SRR10829903" "https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/010576/SRR10829904" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ BioProject : chr [1:10] "PRJNA599088" "PRJNA599088" "PRJNA599088" "PRJNA599088" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 599088 599088 599088 599088 599088 599088 599088 599088 599088 599088
## ..$ Sample : chr [1:10] "SRS5944437" "SRS5944438" "SRS5944439" "SRS5944440" ...
## ..$ BioSample : chr [1:10] "SAMN13738743" "SAMN13738742" "SAMN13738741" "SAMN13738740" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA1020255" "SRA1020255" "SRA1020255" "SRA1020255" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "55BF35373F0257351F0D34C4007B700C" "34ECE45C65E30A81FB49819DA53B7E4F" "A465C6ED4F49CAF25918ECEEA65A3C6F" "7D64256D57958B60FA44F9F018BD303A" ...
## ..$ ReadHash : chr [1:10] "1D9C667121E313B1D4EB6825A7A083C4" "6FF36B70172D786BC1495AFDD4746FA0" "378AA2B084F112D38EF3AD7C15B4B86B" "6269C7E34EDD7660EAAC7C1CEB860FAC" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP239527:Genes expressed differenially in unstimulated healthy donor cells vs type 1 diabetes cells stimulated by Neutrophil extracellular traps from type 1 diabetes cells:HDOunstim; SRX7503269,SRX7503270,SRX7503271,SRX7503272,SRX7503273:T1D+T1DNET; SRX7503294,SRX7503295,SRX7503296,SRX7503297,SRX7503298## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR10829901: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829902: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829903: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829904: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829905: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829926: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829927: int [1:58302] 0 4 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829928: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829929: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829930: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR10829901: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829902: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829903: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829904: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829905: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829926: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829927: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829928: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829929: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829930: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR10829901: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829902: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829903: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829904: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829905: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829926: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829927: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829928: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829929: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829930: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX7503269" "SRX7503270" "SRX7503271" "SRX7503272" ...
## ..$ SRS_accession: chr [1:10] "SRS5944437" "SRS5944438" "SRS5944439" "SRS5944440" ...
## ..$ SRP_accession: chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250898" "GSM4250899" "GSM4250900" "GSM4250901" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX7503269" "SRX7503270" "SRX7503271" "SRX7503272" ...
## ..$ SRS_accession : chr [1:10] "SRS5944437" "SRS5944438" "SRS5944439" "SRS5944440" ...
## ..$ SRP_accession : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250898" "GSM4250899" "GSM4250900" "GSM4250901" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM4250898" "GSM4250899" "GSM4250900" "GSM4250901" ...
## ..$ ReleaseDate : chr [1:10] "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" ...
## ..$ LoadDate : chr [1:10] "2020-01-06 10:18:54" "2020-01-06 10:18:08" "2020-01-06 10:19:25" "2020-01-06 10:18:27" ...
## ..$ spots : int [1:10] 20717200 20108918 22853719 21389517 18892230 17320173 19839460 24009283 26303453 21619721
## ..$ bases : int [1:10] 1056577200 1025554818 1165539669 1090865367 963503730 883328823 1011812460 1224473433 1341476103 1102605771
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 51 51 51 51 51 51 51 51 51 51
## ..$ size_MB : int [1:10] 385 370 419 391 348 320 368 441 482 401
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra7/SRR/010576/SRR10829901" "https://sra-download.ncbi.nlm.nih.gov/traces/sra51/SRR/010576/SRR10829902" "https://sra-download.ncbi.nlm.nih.gov/traces/sra70/SRR/010576/SRR10829903" "https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/010576/SRR10829904" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ BioProject : chr [1:10] "PRJNA599088" "PRJNA599088" "PRJNA599088" "PRJNA599088" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 599088 599088 599088 599088 599088 599088 599088 599088 599088 599088
## ..$ Sample : chr [1:10] "SRS5944437" "SRS5944438" "SRS5944439" "SRS5944440" ...
## ..$ BioSample : chr [1:10] "SAMN13738743" "SAMN13738742" "SAMN13738741" "SAMN13738740" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA1020255" "SRA1020255" "SRA1020255" "SRA1020255" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "55BF35373F0257351F0D34C4007B700C" "34ECE45C65E30A81FB49819DA53B7E4F" "A465C6ED4F49CAF25918ECEEA65A3C6F" "7D64256D57958B60FA44F9F018BD303A" ...
## ..$ ReadHash : chr [1:10] "1D9C667121E313B1D4EB6825A7A083C4" "6FF36B70172D786BC1495AFDD4746FA0" "378AA2B084F112D38EF3AD7C15B4B86B" "6269C7E34EDD7660EAAC7C1CEB860FAC" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP239527:Genes expressed differenially in healthy donor cells stimulated by Neutrophil extracellular traps from healthy donor cells vs unstimulated type 1 diabetes cells:HDO+HDONET; SRX7503274,SRX7503275,SRX7503276,SRX7503277,SRX7503278:T1Dunstim; SRX7503284,SRX7503285,SRX7503286,SRX7503287,SRX7503288## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR10829906: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829907: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829908: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829909: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829910: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829916: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829917: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829918: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829919: int [1:58302] 1 3 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829920: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR10829906: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829907: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829908: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829909: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829910: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829916: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829917: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829918: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829919: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829920: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR10829906: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829907: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829908: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829909: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829910: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829916: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829917: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829918: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829919: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829920: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX7503274" "SRX7503275" "SRX7503276" "SRX7503277" ...
## ..$ SRS_accession: chr [1:10] "SRS5944442" "SRS5944443" "SRS5944444" "SRS5944445" ...
## ..$ SRP_accession: chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250903" "GSM4250904" "GSM4250905" "GSM4250906" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX7503274" "SRX7503275" "SRX7503276" "SRX7503277" ...
## ..$ SRS_accession : chr [1:10] "SRS5944442" "SRS5944443" "SRS5944444" "SRS5944445" ...
## ..$ SRP_accession : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250903" "GSM4250904" "GSM4250905" "GSM4250906" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM4250903" "GSM4250904" "GSM4250905" "GSM4250906" ...
## ..$ ReleaseDate : chr [1:10] "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" ...
## ..$ LoadDate : chr [1:10] "2020-01-06 10:18:50" "2020-01-06 10:19:32" "2020-01-06 10:19:28" "2020-01-06 10:18:21" ...
## ..$ spots : int [1:10] 21125296 23653124 23185534 19399719 19019249 24557483 21599113 22707477 21757324 20717072
## ..$ bases : int [1:10] 1077390096 1206309324 1182462234 989385669 969981699 1252431633 1101554763 1158081327 1109623524 1056570672
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 51 51 51 51 51 51 51 51 51 51
## ..$ size_MB : int [1:10] 391 435 423 357 354 449 400 421 401 383
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra23/SRR/010576/SRR10829906" "https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/010576/SRR10829907" "https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRR/010576/SRR10829908" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/010576/SRR10829909" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ BioProject : chr [1:10] "PRJNA599088" "PRJNA599088" "PRJNA599088" "PRJNA599088" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 599088 599088 599088 599088 599088 599088 599088 599088 599088 599088
## ..$ Sample : chr [1:10] "SRS5944442" "SRS5944443" "SRS5944444" "SRS5944445" ...
## ..$ BioSample : chr [1:10] "SAMN13738738" "SAMN13738737" "SAMN13738736" "SAMN13738735" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA1020255" "SRA1020255" "SRA1020255" "SRA1020255" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "9EAF44D167ED2F763DD106669E5F6451" "B7524723F75DF46EA70D60545CA30DDD" "BDEB22CB1E48291FF22C0E602890E788" "2E83FBC7595B0A5D5208DD7B1462C329" ...
## ..$ ReadHash : chr [1:10] "AA9448135EC63591BA45FAE7F990F849" "3FD7BB4EB945EC0B70D54400048D4BAA" "EEC88A88D22AFDEBB63C49051CD172A9" "E5BEDA72DC34845B73E16F4587AF0CE5" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP239527:Genes expressed differenially in healthy donor cells stimulated by Neutrophil extracellular traps from healthy donor cells vs type 1 diabetes cells stimulated by Neutrophil extracellular traps from healthy donor cells:HDO+HDONET; SRX7503274,SRX7503275,SRX7503276,SRX7503277,SRX7503278:T1D+HDONET;SRX7503289,SRX7503290,SRX7503291,SRX7503292,SRX7503293## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR10829906: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829907: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829908: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829909: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829910: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829921: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829922: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829923: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829924: int [1:58302] 0 3 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829925: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR10829906: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829907: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829908: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829909: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829910: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829921: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829922: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829923: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829924: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829925: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR10829906: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829907: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829908: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829909: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829910: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829921: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829922: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829923: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829924: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829925: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX7503274" "SRX7503275" "SRX7503276" "SRX7503277" ...
## ..$ SRS_accession: chr [1:10] "SRS5944442" "SRS5944443" "SRS5944444" "SRS5944445" ...
## ..$ SRP_accession: chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250903" "GSM4250904" "GSM4250905" "GSM4250906" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX7503274" "SRX7503275" "SRX7503276" "SRX7503277" ...
## ..$ SRS_accession : chr [1:10] "SRS5944442" "SRS5944443" "SRS5944444" "SRS5944445" ...
## ..$ SRP_accession : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250903" "GSM4250904" "GSM4250905" "GSM4250906" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM4250903" "GSM4250904" "GSM4250905" "GSM4250906" ...
## ..$ ReleaseDate : chr [1:10] "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" ...
## ..$ LoadDate : chr [1:10] "2020-01-06 10:18:50" "2020-01-06 10:19:32" "2020-01-06 10:19:28" "2020-01-06 10:18:21" ...
## ..$ spots : int [1:10] 21125296 23653124 23185534 19399719 19019249 18882937 23378418 24869341 19961170 18552981
## ..$ bases : int [1:10] 1077390096 1206309324 1182462234 989385669 969981699 963029787 1192299318 1268336391 1018019670 946202031
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 51 51 51 51 51 51 51 51 51 51
## ..$ size_MB : int [1:10] 391 435 423 357 354 348 432 460 368 344
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra23/SRR/010576/SRR10829906" "https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/010576/SRR10829907" "https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRR/010576/SRR10829908" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/010576/SRR10829909" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ BioProject : chr [1:10] "PRJNA599088" "PRJNA599088" "PRJNA599088" "PRJNA599088" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 599088 599088 599088 599088 599088 599088 599088 599088 599088 599088
## ..$ Sample : chr [1:10] "SRS5944442" "SRS5944443" "SRS5944444" "SRS5944445" ...
## ..$ BioSample : chr [1:10] "SAMN13738738" "SAMN13738737" "SAMN13738736" "SAMN13738735" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA1020255" "SRA1020255" "SRA1020255" "SRA1020255" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "9EAF44D167ED2F763DD106669E5F6451" "B7524723F75DF46EA70D60545CA30DDD" "BDEB22CB1E48291FF22C0E602890E788" "2E83FBC7595B0A5D5208DD7B1462C329" ...
## ..$ ReadHash : chr [1:10] "AA9448135EC63591BA45FAE7F990F849" "3FD7BB4EB945EC0B70D54400048D4BAA" "EEC88A88D22AFDEBB63C49051CD172A9" "E5BEDA72DC34845B73E16F4587AF0CE5" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP239527:Genes expressed differenially in healthy donor cells stimulated by Neutrophil extracellular traps from healthy donor cells vs type 1 diabetes cells stimulated by Neutrophil extracellular traps from type 1 diabetes cells:HDO+HDONET; SRX7503274,SRX7503275,SRX7503276,SRX7503277,SRX7503278:T1D+T1DNET; SRX7503294,SRX7503295,SRX7503296,SRX7503297,SRX7503298## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR10829906: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829907: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829908: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829909: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829910: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829926: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829927: int [1:58302] 0 4 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829928: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829929: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829930: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR10829906: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829907: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829908: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829909: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829910: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829926: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829927: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829928: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829929: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829930: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR10829906: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829907: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829908: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829909: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829910: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829926: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829927: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829928: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829929: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829930: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX7503274" "SRX7503275" "SRX7503276" "SRX7503277" ...
## ..$ SRS_accession: chr [1:10] "SRS5944442" "SRS5944443" "SRS5944444" "SRS5944445" ...
## ..$ SRP_accession: chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250903" "GSM4250904" "GSM4250905" "GSM4250906" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX7503274" "SRX7503275" "SRX7503276" "SRX7503277" ...
## ..$ SRS_accession : chr [1:10] "SRS5944442" "SRS5944443" "SRS5944444" "SRS5944445" ...
## ..$ SRP_accession : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250903" "GSM4250904" "GSM4250905" "GSM4250906" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM4250903" "GSM4250904" "GSM4250905" "GSM4250906" ...
## ..$ ReleaseDate : chr [1:10] "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:26" ...
## ..$ LoadDate : chr [1:10] "2020-01-06 10:18:50" "2020-01-06 10:19:32" "2020-01-06 10:19:28" "2020-01-06 10:18:21" ...
## ..$ spots : int [1:10] 21125296 23653124 23185534 19399719 19019249 17320173 19839460 24009283 26303453 21619721
## ..$ bases : int [1:10] 1077390096 1206309324 1182462234 989385669 969981699 883328823 1011812460 1224473433 1341476103 1102605771
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 51 51 51 51 51 51 51 51 51 51
## ..$ size_MB : int [1:10] 391 435 423 357 354 320 368 441 482 401
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra23/SRR/010576/SRR10829906" "https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/010576/SRR10829907" "https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRR/010576/SRR10829908" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/010576/SRR10829909" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ BioProject : chr [1:10] "PRJNA599088" "PRJNA599088" "PRJNA599088" "PRJNA599088" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 599088 599088 599088 599088 599088 599088 599088 599088 599088 599088
## ..$ Sample : chr [1:10] "SRS5944442" "SRS5944443" "SRS5944444" "SRS5944445" ...
## ..$ BioSample : chr [1:10] "SAMN13738738" "SAMN13738737" "SAMN13738736" "SAMN13738735" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA1020255" "SRA1020255" "SRA1020255" "SRA1020255" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "9EAF44D167ED2F763DD106669E5F6451" "B7524723F75DF46EA70D60545CA30DDD" "BDEB22CB1E48291FF22C0E602890E788" "2E83FBC7595B0A5D5208DD7B1462C329" ...
## ..$ ReadHash : chr [1:10] "AA9448135EC63591BA45FAE7F990F849" "3FD7BB4EB945EC0B70D54400048D4BAA" "EEC88A88D22AFDEBB63C49051CD172A9" "E5BEDA72DC34845B73E16F4587AF0CE5" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP239527:Genes expressed differenially in healthy donor cells stimulated by Neutrophil extracellular traps from type 1 diabetes cells vs unstimulated type 1 diabetes cells:HDO+T1DNET; SRX7503279,SRX7503280,SRX7503281,SRX7503282,SRX7503283:T1Dunstim; SRX7503284,SRX7503285,SRX7503286,SRX7503287,SRX7503288## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR10829911: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829912: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829913: int [1:58302] 0 2 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829914: int [1:58302] 0 0 0 0 0 0 0 0 0 3 ...
## ..$ SRR10829915: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829916: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829917: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829918: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829919: int [1:58302] 1 3 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829920: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR10829911: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829912: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829913: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829914: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829915: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829916: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829917: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829918: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829919: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829920: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR10829911: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829912: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829913: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829914: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829915: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829916: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829917: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829918: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829919: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829920: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX7503279" "SRX7503280" "SRX7503281" "SRX7503282" ...
## ..$ SRS_accession: chr [1:10] "SRS5944447" "SRS5944448" "SRS5944449" "SRS5944450" ...
## ..$ SRP_accession: chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250908" "GSM4250909" "GSM4250910" "GSM4250911" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX7503279" "SRX7503280" "SRX7503281" "SRX7503282" ...
## ..$ SRS_accession : chr [1:10] "SRS5944447" "SRS5944448" "SRS5944449" "SRS5944450" ...
## ..$ SRP_accession : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250908" "GSM4250909" "GSM4250910" "GSM4250911" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM4250908" "GSM4250909" "GSM4250910" "GSM4250911" ...
## ..$ ReleaseDate : chr [1:10] "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:27" "2020-01-07 18:26:27" ...
## ..$ LoadDate : chr [1:10] "2020-01-06 10:19:57" "2020-01-06 10:19:50" "2020-01-06 10:18:41" "2020-01-06 10:19:38" ...
## ..$ spots : int [1:10] 24604945 24181273 20152489 21998460 16189586 24557483 21599113 22707477 21757324 20717072
## ..$ bases : int [1:10] 1254852195 1233244923 1027776939 1121921460 825668886 1252431633 1101554763 1158081327 1109623524 1056570672
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 51 51 51 51 51 51 51 51 51 51
## ..$ size_MB : int [1:10] 453 443 373 406 298 449 400 421 401 383
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/010576/SRR10829911" "https://sra-download.ncbi.nlm.nih.gov/traces/sra8/SRR/010576/SRR10829912" "https://sra-download.ncbi.nlm.nih.gov/traces/sra46/SRR/010576/SRR10829913" "https://sra-download.ncbi.nlm.nih.gov/traces/sra14/SRR/010576/SRR10829914" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ BioProject : chr [1:10] "PRJNA599088" "PRJNA599088" "PRJNA599088" "PRJNA599088" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 599088 599088 599088 599088 599088 599088 599088 599088 599088 599088
## ..$ Sample : chr [1:10] "SRS5944447" "SRS5944448" "SRS5944449" "SRS5944450" ...
## ..$ BioSample : chr [1:10] "SAMN13738733" "SAMN13738732" "SAMN13738731" "SAMN13738730" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA1020255" "SRA1020255" "SRA1020255" "SRA1020255" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "148369481590B5F4FDB60BD52E2C7135" "F54093FFCAF98045940C1B386C5A46F9" "8F4210DFD655F7E018224BA2F8EFA94D" "DE45F3E79791A31CF93975D25C1A5977" ...
## ..$ ReadHash : chr [1:10] "F5A22EE2F95E6E77B442DE25502A63DC" "F83D6DA7B9F7E7666FF876191D1C0B48" "96B35C26328BDA23A121C77912517435" "E237DEAE22AEEA0F6A0BDFE59DA6D600" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP239527:Genes expressed differenially in healthy donor cells stimulated by Neutrophil extracellular traps from type 1 diabetes cells vs type 1 diabetes cells stimulated by Neutrophil extracellular traps from healthy donor cells:HDO+T1DNET; SRX7503279,SRX7503280,SRX7503281,SRX7503282,SRX7503283:T1D+HDONET;SRX7503289,SRX7503290,SRX7503291,SRX7503292,SRX7503293## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR10829911: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829912: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829913: int [1:58302] 0 2 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829914: int [1:58302] 0 0 0 0 0 0 0 0 0 3 ...
## ..$ SRR10829915: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829921: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829922: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829923: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829924: int [1:58302] 0 3 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829925: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR10829911: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829912: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829913: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829914: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829915: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829921: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829922: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829923: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829924: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829925: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR10829911: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829912: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829913: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829914: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829915: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829921: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829922: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829923: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829924: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829925: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX7503279" "SRX7503280" "SRX7503281" "SRX7503282" ...
## ..$ SRS_accession: chr [1:10] "SRS5944447" "SRS5944448" "SRS5944449" "SRS5944450" ...
## ..$ SRP_accession: chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250908" "GSM4250909" "GSM4250910" "GSM4250911" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX7503279" "SRX7503280" "SRX7503281" "SRX7503282" ...
## ..$ SRS_accession : chr [1:10] "SRS5944447" "SRS5944448" "SRS5944449" "SRS5944450" ...
## ..$ SRP_accession : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250908" "GSM4250909" "GSM4250910" "GSM4250911" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM4250908" "GSM4250909" "GSM4250910" "GSM4250911" ...
## ..$ ReleaseDate : chr [1:10] "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:27" "2020-01-07 18:26:27" ...
## ..$ LoadDate : chr [1:10] "2020-01-06 10:19:57" "2020-01-06 10:19:50" "2020-01-06 10:18:41" "2020-01-06 10:19:38" ...
## ..$ spots : int [1:10] 24604945 24181273 20152489 21998460 16189586 18882937 23378418 24869341 19961170 18552981
## ..$ bases : int [1:10] 1254852195 1233244923 1027776939 1121921460 825668886 963029787 1192299318 1268336391 1018019670 946202031
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 51 51 51 51 51 51 51 51 51 51
## ..$ size_MB : int [1:10] 453 443 373 406 298 348 432 460 368 344
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/010576/SRR10829911" "https://sra-download.ncbi.nlm.nih.gov/traces/sra8/SRR/010576/SRR10829912" "https://sra-download.ncbi.nlm.nih.gov/traces/sra46/SRR/010576/SRR10829913" "https://sra-download.ncbi.nlm.nih.gov/traces/sra14/SRR/010576/SRR10829914" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ BioProject : chr [1:10] "PRJNA599088" "PRJNA599088" "PRJNA599088" "PRJNA599088" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 599088 599088 599088 599088 599088 599088 599088 599088 599088 599088
## ..$ Sample : chr [1:10] "SRS5944447" "SRS5944448" "SRS5944449" "SRS5944450" ...
## ..$ BioSample : chr [1:10] "SAMN13738733" "SAMN13738732" "SAMN13738731" "SAMN13738730" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA1020255" "SRA1020255" "SRA1020255" "SRA1020255" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "148369481590B5F4FDB60BD52E2C7135" "F54093FFCAF98045940C1B386C5A46F9" "8F4210DFD655F7E018224BA2F8EFA94D" "DE45F3E79791A31CF93975D25C1A5977" ...
## ..$ ReadHash : chr [1:10] "F5A22EE2F95E6E77B442DE25502A63DC" "F83D6DA7B9F7E7666FF876191D1C0B48" "96B35C26328BDA23A121C77912517435" "E237DEAE22AEEA0F6A0BDFE59DA6D600" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP239527:Genes expressed differenially in healthy donor cells stimulated by Neutrophil extracellular traps from type 1 diabetes cells vs type 1 diabetes cells stimulated by Neutrophil extracellular traps from type 1 diabetes cells:HDO+T1DNET; SRX7503279,SRX7503280,SRX7503281,SRX7503282,SRX7503283:T1D+T1DNET; SRX7503294,SRX7503295,SRX7503296,SRX7503297,SRX7503298## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR10829911: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829912: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829913: int [1:58302] 0 2 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829914: int [1:58302] 0 0 0 0 0 0 0 0 0 3 ...
## ..$ SRR10829915: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829926: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829927: int [1:58302] 0 4 0 0 0 0 0 0 0 1 ...
## ..$ SRR10829928: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829929: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829930: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR10829911: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829912: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829913: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829914: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829915: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829926: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829927: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829928: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829929: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10829930: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR10829911: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829912: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829913: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829914: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829915: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829926: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829927: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829928: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829929: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR10829930: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX7503279" "SRX7503280" "SRX7503281" "SRX7503282" ...
## ..$ SRS_accession: chr [1:10] "SRS5944447" "SRS5944448" "SRS5944449" "SRS5944450" ...
## ..$ SRP_accession: chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250908" "GSM4250909" "GSM4250910" "GSM4250911" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX7503279" "SRX7503280" "SRX7503281" "SRX7503282" ...
## ..$ SRS_accession : chr [1:10] "SRS5944447" "SRS5944448" "SRS5944449" "SRS5944450" ...
## ..$ SRP_accession : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ Sample_name : chr [1:10] "GSM4250908" "GSM4250909" "GSM4250910" "GSM4250911" ...
## ..$ GEO_series : chr [1:10] "GSE143143" "GSE143143" "GSE143143" "GSE143143" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM4250908" "GSM4250909" "GSM4250910" "GSM4250911" ...
## ..$ ReleaseDate : chr [1:10] "2020-01-07 18:26:26" "2020-01-07 18:26:26" "2020-01-07 18:26:27" "2020-01-07 18:26:27" ...
## ..$ LoadDate : chr [1:10] "2020-01-06 10:19:57" "2020-01-06 10:19:50" "2020-01-06 10:18:41" "2020-01-06 10:19:38" ...
## ..$ spots : int [1:10] 24604945 24181273 20152489 21998460 16189586 17320173 19839460 24009283 26303453 21619721
## ..$ bases : int [1:10] 1254852195 1233244923 1027776939 1121921460 825668886 883328823 1011812460 1224473433 1341476103 1102605771
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 51 51 51 51 51 51 51 51 51 51
## ..$ size_MB : int [1:10] 453 443 373 406 298 320 368 441 482 401
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/010576/SRR10829911" "https://sra-download.ncbi.nlm.nih.gov/traces/sra8/SRR/010576/SRR10829912" "https://sra-download.ncbi.nlm.nih.gov/traces/sra46/SRR/010576/SRR10829913" "https://sra-download.ncbi.nlm.nih.gov/traces/sra14/SRR/010576/SRR10829914" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP239527" "SRP239527" "SRP239527" "SRP239527" ...
## ..$ BioProject : chr [1:10] "PRJNA599088" "PRJNA599088" "PRJNA599088" "PRJNA599088" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 599088 599088 599088 599088 599088 599088 599088 599088 599088 599088
## ..$ Sample : chr [1:10] "SRS5944447" "SRS5944448" "SRS5944449" "SRS5944450" ...
## ..$ BioSample : chr [1:10] "SAMN13738733" "SAMN13738732" "SAMN13738731" "SAMN13738730" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA1020255" "SRA1020255" "SRA1020255" "SRA1020255" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "148369481590B5F4FDB60BD52E2C7135" "F54093FFCAF98045940C1B386C5A46F9" "8F4210DFD655F7E018224BA2F8EFA94D" "DE45F3E79791A31CF93975D25C1A5977" ...
## ..$ ReadHash : chr [1:10] "F5A22EE2F95E6E77B442DE25502A63DC" "F83D6DA7B9F7E7666FF876191D1C0B48" "96B35C26328BDA23A121C77912517435" "E237DEAE22AEEA0F6A0BDFE59DA6D600" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP035268:Genes expressed differentially regulated by saturated fatty acids in Pancreatic beta-cells:Ctrl;SRX424352, SRX424354,SRX424356,SRX424358,SRX424360:SFA;SRX424353,SRX424355,SRX424357,SRX424359,SRX424361,## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR1105566: int [1:58302] 0 2 2 0 0 0 0 0 0 1 ...
## ..$ SRR1105567: int [1:58302] 0 0 11 0 0 0 0 0 0 0 ...
## ..$ SRR1105568: int [1:58302] 0 6 16 0 0 0 0 0 0 0 ...
## ..$ SRR1105569: int [1:58302] 1 5 11 0 0 0 0 0 0 0 ...
## ..$ SRR1105570: int [1:58302] 0 8 32 0 0 0 0 0 0 0 ...
## ..$ SRR1105571: int [1:58302] 0 15 35 0 0 0 0 0 0 1 ...
## ..$ SRR1105572: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR1105573: int [1:58302] 0 2 7 0 0 0 0 0 0 0 ...
## ..$ SRR1105574: int [1:58302] 0 12 22 0 0 0 0 0 0 1 ...
## ..$ SRR1105575: int [1:58302] 0 0 9 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR1105566: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1105567: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1105568: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1105569: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1105570: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1105571: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1105572: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1105573: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1105574: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1105575: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR1105566: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1105567: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1105568: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1105569: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1105570: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1105571: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1105572: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1105573: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1105574: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1105575: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "WARN(1,5,7)" "WARN(1,5,7)" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX424352" "SRX424353" "SRX424354" "SRX424355" ...
## ..$ SRS_accession: chr [1:10] "SRS528028" "SRS528029" "SRS528031" "SRS528030" ...
## ..$ SRP_accession: chr [1:10] "SRP035268" "SRP035268" "SRP035268" "SRP035268" ...
## ..$ Sample_name : chr [1:10] "GSM1303926" "GSM1303927" "GSM1303928" "GSM1303929" ...
## ..$ GEO_series : chr [1:10] "GSE53949" "GSE53949" "GSE53949" "GSE53949" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "WARN(1,5,7)" "WARN(1,5,7)" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX424352" "SRX424353" "SRX424354" "SRX424355" ...
## ..$ SRS_accession : chr [1:10] "SRS528028" "SRS528029" "SRS528031" "SRS528030" ...
## ..$ SRP_accession : chr [1:10] "SRP035268" "SRP035268" "SRP035268" "SRP035268" ...
## ..$ Sample_name : chr [1:10] "GSM1303926" "GSM1303927" "GSM1303928" "GSM1303929" ...
## ..$ GEO_series : chr [1:10] "GSE53949" "GSE53949" "GSE53949" "GSE53949" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM1303926" "GSM1303927" "GSM1303928" "GSM1303929" ...
## ..$ ReleaseDate : chr [1:10] "2015-07-22 17:04:31" "2015-07-22 17:04:31" "2015-07-22 17:04:31" "2015-07-22 17:04:31" ...
## ..$ LoadDate : chr [1:10] "2015-12-09 08:30:20" "2015-12-11 14:00:19" "2015-12-09 08:39:56" "2015-12-11 14:07:19" ...
## ..$ spots : int [1:10] 6785237 6300019 29665483 29556299 28702757 33066401 11538404 18603348 25717722 4380242
## ..$ bases : num [1:10] 6.92e+08 6.43e+08 3.03e+09 3.01e+09 2.93e+09 ...
## ..$ spots_with_mates : int [1:10] 6785237 6300019 29665483 29556299 28702757 33066401 11538404 18603348 25717722 4380242
## ..$ avgLength : int [1:10] 102 102 102 102 102 102 102 102 102 102
## ..$ size_MB : int [1:10] 443 410 1178 1186 1117 1280 755 1259 1151 276
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1105566/SRR1105566.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1105567/SRR1105567.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1105568/SRR1105568.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1105569/SRR1105569.2" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina Genome Analyzer II" "Illumina Genome Analyzer II" "Illumina Genome Analyzer II" "Illumina Genome Analyzer II" ...
## ..$ SRAStudy : chr [1:10] "SRP035268" "SRP035268" "SRP035268" "SRP035268" ...
## ..$ BioProject : chr [1:10] "PRJNA234026" "PRJNA234026" "PRJNA234026" "PRJNA234026" ...
## ..$ Study_Pubmed_id : int [1:10] 2 2 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:10] 234026 234026 234026 234026 234026 234026 234026 234026 234026 234026
## ..$ Sample : chr [1:10] "SRS528028" "SRS528029" "SRS528031" "SRS528030" ...
## ..$ BioSample : chr [1:10] "SAMN02580441" "SAMN02580444" "SAMN02580438" "SAMN02580434" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA123968" "SRA123968" "SRA123968" "SRA123968" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "FAE82E180B667D4CD696DB8CB770913C" "06E37CFC1E0F7CEBE5A1999A2D733807" "46642BB150F3C0FA83DD65BF91092EA3" "A0FDEF054EAB491726B31131450E2834" ...
## ..$ ReadHash : chr [1:10] "9267DAAA0DD36698D09CA4780DDAE451" "B9156DB18D20D8BAB5DB187A457F6451" "A1D6525B7420E5DBCA84A3D5DDA5FC69" "6350D900EC37523CFC438A4300CE6F80" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP230455:Genes expressed differentially in those that have type 1 diabetes and have declining renal functionality and healthy individuals:Ctrl;SRX7177515,SRX7177516:Decliners; SRX7177517,SRX7177518,SRX7177522,SRX7177524## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR10488341: int [1:58302] 0 0 3 0 0 0 0 0 1 2 ...
## ..$ SRR10488342: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR10488343: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR10488344: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR10488348: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR10488350: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR10488341: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10488342: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10488343: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10488344: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10488348: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10488350: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR10488341: chr [1:30] "PE" "Sanger/Illumina1.9" "39" "101" ...
## ..$ SRR10488342: chr [1:30] "PE" "Sanger/Illumina1.9" "52" "101" ...
## ..$ SRR10488343: chr [1:30] "PE" "Sanger/Illumina1.9" "39" "101" ...
## ..$ SRR10488344: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "101" ...
## ..$ SRR10488348: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "101" ...
## ..$ SRR10488350: chr [1:30] "PE" "Sanger/Illumina1.9" "44" "101" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(6)" "WARN(5,6,7,8)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" ...
## ..$ SRX_accession: chr [1:6] "SRX7177515" "SRX7177516" "SRX7177517" "SRX7177518" ...
## ..$ SRS_accession: chr [1:6] "SRS5684491" "SRS5684492" "SRS5684493" "SRS5684494" ...
## ..$ SRP_accession: chr [1:6] "SRP230455" "SRP230455" "SRP230455" "SRP230455" ...
## ..$ Sample_name : chr [1:6] "GSM4175969" "GSM4175970" "GSM4175971" "GSM4175972" ...
## ..$ GEO_series : chr [1:6] "GSE140627" "GSE140627" "GSE140627" "GSE140627" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "FAIL(6)" "WARN(5,6,7,8)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" ...
## ..$ SRX_accession : chr [1:6] "SRX7177515" "SRX7177516" "SRX7177517" "SRX7177518" ...
## ..$ SRS_accession : chr [1:6] "SRS5684491" "SRS5684492" "SRS5684493" "SRS5684494" ...
## ..$ SRP_accession : chr [1:6] "SRP230455" "SRP230455" "SRP230455" "SRP230455" ...
## ..$ Sample_name : chr [1:6] "GSM4175969" "GSM4175970" "GSM4175971" "GSM4175972" ...
## ..$ GEO_series : chr [1:6] "GSE140627" "GSE140627" "GSE140627" "GSE140627" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4175969" "GSM4175970" "GSM4175971" "GSM4175972" ...
## ..$ ReleaseDate : chr [1:6] "2019-11-21 01:06:25" "2019-11-21 01:06:25" "2019-11-21 01:06:25" "2019-11-21 01:06:25" ...
## ..$ LoadDate : chr [1:6] "2019-11-19 04:56:47" "2019-11-19 04:57:02" "2019-11-19 05:03:09" "2019-11-19 05:02:23" ...
## ..$ spots : int [1:6] 14272730 11915332 21790340 22809613 13814026 14131647
## ..$ bases : num [1:6] 2.84e+09 2.37e+09 4.36e+09 4.56e+09 2.76e+09 ...
## ..$ spots_with_mates : int [1:6] 14272730 11915332 21790340 22809613 13814026 14131647
## ..$ avgLength : int [1:6] 198 198 200 200 199 199
## ..$ size_MB : int [1:6] 1359 1118 2064 2167 1320 1336
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra11/SRR/010242/SRR10488341" "https://sra-download.ncbi.nlm.nih.gov/traces/sra33/SRR/010242/SRR10488342" "https://sra-download.ncbi.nlm.nih.gov/traces/sra33/SRR/010242/SRR10488343" "https://sra-download.ncbi.nlm.nih.gov/traces/sra33/SRR/010242/SRR10488344" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP230455" "SRP230455" "SRP230455" "SRP230455" ...
## ..$ BioProject : chr [1:6] "PRJNA590268" "PRJNA590268" "PRJNA590268" "PRJNA590268" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 590268 590268 590268 590268 590268 590268
## ..$ Sample : chr [1:6] "SRS5684491" "SRS5684492" "SRS5684493" "SRS5684494" ...
## ..$ BioSample : chr [1:6] "SAMN13323614" "SAMN13323613" "SAMN13323612" "SAMN13323611" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA998061" "SRA998061" "SRA998061" "SRA998061" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "36E5BB87B9DB8AB17069B333D1A0268D" "F1D909568E672E903CC2295DD996C95D" "7BEB77C69E42FBB2B1F9263B8BE22077" "E8D2CB67FEA66F6FB5E5A8D394812ECC" ...
## ..$ ReadHash : chr [1:6] "3F970405698B90B5BEDCB5F01A2EB968" "4894C2D0DAC6A0BA0C460E10D9BAA5D7" "9B966C00BE92AFF90F4E2840A2001D1C" "F2E380CF7841BBFF219868E4EFCD817E" ...
## $ absent : chr(0)## SRP042186: Genes expressed differentially regulated by treatment of human white adipose tissue with 24 hours of JAK inhibition:Ctrl; SRX550549,SRX550550,SRX550551:WATJAKinhibitortreatment24hr; SRX550552,SRX550553,SRX550554
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR1296118: int [1:58302] 1 12 2 1 0 0 0 0 0 1 ...
## ..$ SRR1296119: int [1:58302] 1 7 2 1 0 0 0 0 0 0 ...
## ..$ SRR1296120: int [1:58302] 0 15 4 0 0 0 0 0 0 1 ...
## ..$ SRR1296121: int [1:58302] 0 11 2 0 0 0 0 0 0 1 ...
## ..$ SRR1296122: int [1:58302] 1 8 4 1 0 0 0 0 0 0 ...
## ..$ SRR1296123: int [1:58302] 0 12 4 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1296118: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296119: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296120: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296121: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296122: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296123: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR1296118: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296119: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296120: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296121: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296122: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296123: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "WARN(8)" ...
## ..$ SRX_accession: chr [1:6] "SRX550549" "SRX550550" "SRX550551" "SRX550552" ...
## ..$ SRS_accession: chr [1:6] "SRS618290" "SRS618291" "SRS618292" "SRS618293" ...
## ..$ SRP_accession: chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ Sample_name : chr [1:6] "GSM1396721" "GSM1396722" "GSM1396723" "GSM1396724" ...
## ..$ GEO_series : chr [1:6] "GSE57896" "GSE57896" "GSE57896" "GSE57896" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "WARN(8)" ...
## ..$ SRX_accession : chr [1:6] "SRX550549" "SRX550550" "SRX550551" "SRX550552" ...
## ..$ SRS_accession : chr [1:6] "SRS618290" "SRS618291" "SRS618292" "SRS618293" ...
## ..$ SRP_accession : chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ Sample_name : chr [1:6] "GSM1396721" "GSM1396722" "GSM1396723" "GSM1396724" ...
## ..$ GEO_series : chr [1:6] "GSE57896" "GSE57896" "GSE57896" "GSE57896" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1396721" "GSM1396722" "GSM1396723" "GSM1396724" ...
## ..$ ReleaseDate : chr [1:6] "2014-11-03 08:58:11" "2014-11-03 08:58:11" "2014-11-03 08:58:11" "2014-11-03 08:58:11" ...
## ..$ LoadDate : chr [1:6] "2014-05-22 13:11:42" "2014-05-22 13:11:04" "2014-05-22 13:14:24" "2014-05-22 13:13:15" ...
## ..$ spots : int [1:6] 34149811 38262101 53895658 42312435 37022851 31442973
## ..$ bases : num [1:6] 3.48e+09 3.90e+09 5.50e+09 4.32e+09 3.78e+09 ...
## ..$ spots_with_mates : int [1:6] 34149811 38262101 53895658 42312435 37022851 31442973
## ..$ avgLength : int [1:6] 102 102 102 102 102 102
## ..$ size_MB : int [1:6] 2044 2290 3234 2512 2221 1879
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296118/SRR1296118.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296119/SRR1296119.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296120/SRR1296120.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296121/SRR1296121.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ BioProject : chr [1:6] "PRJNA248376" "PRJNA248376" "PRJNA248376" "PRJNA248376" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 248376 248376 248376 248376 248376 248376
## ..$ Sample : chr [1:6] "SRS618290" "SRS618291" "SRS618292" "SRS618293" ...
## ..$ BioSample : chr [1:6] "SAMN02798065" "SAMN02798067" "SAMN02798068" "SAMN02798063" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA166790" "SRA166790" "SRA166790" "SRA166790" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "64458EB4A404CFB913E0646E670101BA" "985497D212662774B4BDE9859D1E28D0" "00D7C07EF1BC3B0AEE80A0A315FFF460" "58A9125860EB138B5A983A6259708E96" ...
## ..$ ReadHash : chr [1:6] "F255D6376DE2F3D6E4D706E80D975C21" "E8D27B4B5795AC99B2EDF5BA406A4AB3" "89E69D12D319BD0F21620C94848E4C84" "9C3F1E5E57CC97434195929E96956A1A" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP042186: Genes expressed differentially regulated by treatment of human white adipose tissue with 24 hours of SYK inhibition:Ctrl; SRX550549,SRX550550,SRX550551:WATSYKinhibitortreatment24hr; SRX550555,SRX550556,SRX550557## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR1296118: int [1:58302] 1 12 2 1 0 0 0 0 0 1 ...
## ..$ SRR1296119: int [1:58302] 1 7 2 1 0 0 0 0 0 0 ...
## ..$ SRR1296120: int [1:58302] 0 15 4 0 0 0 0 0 0 1 ...
## ..$ SRR1296124: int [1:58302] 0 9 2 1 0 0 0 0 0 1 ...
## ..$ SRR1296125: int [1:58302] 0 14 4 0 0 0 0 0 0 0 ...
## ..$ SRR1296126: int [1:58302] 0 4 4 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1296118: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296119: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296120: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296124: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296125: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296126: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR1296118: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296119: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296120: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296124: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296125: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296126: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX550549" "SRX550550" "SRX550551" "SRX550555" ...
## ..$ SRS_accession: chr [1:6] "SRS618290" "SRS618291" "SRS618292" "SRS618296" ...
## ..$ SRP_accession: chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ Sample_name : chr [1:6] "GSM1396721" "GSM1396722" "GSM1396723" "GSM1396727" ...
## ..$ GEO_series : chr [1:6] "GSE57896" "GSE57896" "GSE57896" "GSE57896" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX550549" "SRX550550" "SRX550551" "SRX550555" ...
## ..$ SRS_accession : chr [1:6] "SRS618290" "SRS618291" "SRS618292" "SRS618296" ...
## ..$ SRP_accession : chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ Sample_name : chr [1:6] "GSM1396721" "GSM1396722" "GSM1396723" "GSM1396727" ...
## ..$ GEO_series : chr [1:6] "GSE57896" "GSE57896" "GSE57896" "GSE57896" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1396721" "GSM1396722" "GSM1396723" "GSM1396727" ...
## ..$ ReleaseDate : chr [1:6] "2014-11-03 08:58:11" "2014-11-03 08:58:11" "2014-11-03 08:58:11" "2014-11-03 08:58:11" ...
## ..$ LoadDate : chr [1:6] "2014-05-22 13:11:42" "2014-05-22 13:11:04" "2014-05-22 13:14:24" "2014-05-22 13:11:01" ...
## ..$ spots : int [1:6] 34149811 38262101 53895658 32409431 46570020 34357602
## ..$ bases : num [1:6] 3.48e+09 3.90e+09 5.50e+09 3.31e+09 4.75e+09 ...
## ..$ spots_with_mates : int [1:6] 34149811 38262101 53895658 32409431 46570020 34357602
## ..$ avgLength : int [1:6] 102 102 102 102 102 102
## ..$ size_MB : int [1:6] 2044 2290 3234 1916 2800 2040
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296118/SRR1296118.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296119/SRR1296119.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296120/SRR1296120.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296124/SRR1296124.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ BioProject : chr [1:6] "PRJNA248376" "PRJNA248376" "PRJNA248376" "PRJNA248376" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 248376 248376 248376 248376 248376 248376
## ..$ Sample : chr [1:6] "SRS618290" "SRS618291" "SRS618292" "SRS618296" ...
## ..$ BioSample : chr [1:6] "SAMN02798065" "SAMN02798067" "SAMN02798068" "SAMN02798064" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA166790" "SRA166790" "SRA166790" "SRA166790" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "64458EB4A404CFB913E0646E670101BA" "985497D212662774B4BDE9859D1E28D0" "00D7C07EF1BC3B0AEE80A0A315FFF460" "E5C2E37BB5A1D668A1B0A1443A2EFECD" ...
## ..$ ReadHash : chr [1:6] "F255D6376DE2F3D6E4D706E80D975C21" "E8D27B4B5795AC99B2EDF5BA406A4AB3" "89E69D12D319BD0F21620C94848E4C84" "D2872D687B777421F7A19758ED0073D3" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP042186: Genes expressed differentially regulated by treatment of human white adipose tissue with 7 days of JAK inhibition:Ctrl; SRX550564,SRX550565,SRX550566:WATJAKinhibitortreatment7day; SRX550567,SRX550568,SRX550569## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR1296133: int [1:58302] 1 16 2 0 0 0 0 0 0 1 ...
## ..$ SRR1296134: int [1:58302] 0 9 2 0 0 0 0 0 0 0 ...
## ..$ SRR1296135: int [1:58302] 0 14 2 0 0 0 0 0 0 0 ...
## ..$ SRR1296136: int [1:58302] 0 12 1 0 0 0 0 0 0 4 ...
## ..$ SRR1296137: int [1:58302] 1 15 0 1 0 0 0 0 0 0 ...
## ..$ SRR1296138: int [1:58302] 0 17 4 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1296133: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296134: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296135: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296136: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296137: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296138: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR1296133: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296134: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296135: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296136: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296137: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296138: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:6] "SRX550564" "SRX550565" "SRX550566" "SRX550567" ...
## ..$ SRS_accession: chr [1:6] "SRS618305" "SRS618306" "SRS618307" "SRS618308" ...
## ..$ SRP_accession: chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ Sample_name : chr [1:6] "GSM1396736" "GSM1396737" "GSM1396738" "GSM1396739" ...
## ..$ GEO_series : chr [1:6] "GSE57896" "GSE57896" "GSE57896" "GSE57896" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:6] "SRX550564" "SRX550565" "SRX550566" "SRX550567" ...
## ..$ SRS_accession : chr [1:6] "SRS618305" "SRS618306" "SRS618307" "SRS618308" ...
## ..$ SRP_accession : chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ Sample_name : chr [1:6] "GSM1396736" "GSM1396737" "GSM1396738" "GSM1396739" ...
## ..$ GEO_series : chr [1:6] "GSE57896" "GSE57896" "GSE57896" "GSE57896" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1396736" "GSM1396737" "GSM1396738" "GSM1396739" ...
## ..$ ReleaseDate : chr [1:6] "2014-11-03 08:58:11" "2014-11-03 08:58:11" "2014-11-03 08:58:11" "2014-11-03 08:58:11" ...
## ..$ LoadDate : chr [1:6] "2014-05-22 13:37:10" "2014-05-22 13:23:37" "2014-05-22 13:23:06" "2014-05-22 13:25:42" ...
## ..$ spots : int [1:6] 53731689 35599757 36461836 44784084 42928808 42177038
## ..$ bases : num [1:6] 5.48e+09 3.63e+09 3.72e+09 4.57e+09 4.38e+09 ...
## ..$ spots_with_mates : int [1:6] 53731689 35599757 36461836 44784084 42928808 42177038
## ..$ avgLength : int [1:6] 102 102 102 102 102 102
## ..$ size_MB : int [1:6] 3199 2124 2168 2617 2554 2490
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296133/SRR1296133.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296134/SRR1296134.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296135/SRR1296135.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296136/SRR1296136.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ BioProject : chr [1:6] "PRJNA248376" "PRJNA248376" "PRJNA248376" "PRJNA248376" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 248376 248376 248376 248376 248376 248376
## ..$ Sample : chr [1:6] "SRS618305" "SRS618306" "SRS618307" "SRS618308" ...
## ..$ BioSample : chr [1:6] "SAMN02798072" "SAMN02798080" "SAMN02798077" "SAMN02798079" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA166790" "SRA166790" "SRA166790" "SRA166790" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "ADCBB109469D3C7AA05EDA53049761C2" "D116BBF6679740971897ADBE7DB9E2FD" "5803894B2C76ECB37FA2AE4CD636FB48" "0A96819CE2174938888DBB15D568A714" ...
## ..$ ReadHash : chr [1:6] "0624C1859450C2507EE19A22D9FB3421" "0BA4D3A86930F2F334E786F373E9F1C0" "7A231A53FFC75AA3229F03A529D64DA2" "7AF899F328BE8E00C7C733CDE901352B" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP042186: Genes expressed differentially regulated by treatment of human white adipose tissue with 7 days of SYK inhibition:Ctrl; SRX550564,SRX550565,SRX550566:WATSYKinhibitortreatment7day;SRX550570,SRX550571,SRX550572## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR1296133: int [1:58302] 1 16 2 0 0 0 0 0 0 1 ...
## ..$ SRR1296134: int [1:58302] 0 9 2 0 0 0 0 0 0 0 ...
## ..$ SRR1296135: int [1:58302] 0 14 2 0 0 0 0 0 0 0 ...
## ..$ SRR1296139: int [1:58302] 0 14 2 0 0 0 0 0 0 2 ...
## ..$ SRR1296140: int [1:58302] 1 7 6 2 0 0 0 0 0 0 ...
## ..$ SRR1296141: int [1:58302] 0 9 3 2 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1296133: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296134: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296135: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296139: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296140: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296141: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR1296133: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296134: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296135: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296139: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296140: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296141: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:6] "SRX550564" "SRX550565" "SRX550566" "SRX550570" ...
## ..$ SRS_accession: chr [1:6] "SRS618305" "SRS618306" "SRS618307" "SRS618311" ...
## ..$ SRP_accession: chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ Sample_name : chr [1:6] "GSM1396736" "GSM1396737" "GSM1396738" "GSM1396742" ...
## ..$ GEO_series : chr [1:6] "GSE57896" "GSE57896" "GSE57896" "GSE57896" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:6] "SRX550564" "SRX550565" "SRX550566" "SRX550570" ...
## ..$ SRS_accession : chr [1:6] "SRS618305" "SRS618306" "SRS618307" "SRS618311" ...
## ..$ SRP_accession : chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ Sample_name : chr [1:6] "GSM1396736" "GSM1396737" "GSM1396738" "GSM1396742" ...
## ..$ GEO_series : chr [1:6] "GSE57896" "GSE57896" "GSE57896" "GSE57896" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1396736" "GSM1396737" "GSM1396738" "GSM1396742" ...
## ..$ ReleaseDate : chr [1:6] "2014-11-03 08:58:11" "2014-11-03 08:58:11" "2014-11-03 08:58:11" "2014-11-03 08:58:11" ...
## ..$ LoadDate : chr [1:6] "2014-05-22 13:37:10" "2014-05-22 13:23:37" "2014-05-22 13:23:06" "2014-05-22 13:26:54" ...
## ..$ spots : int [1:6] 53731689 35599757 36461836 36921253 53694963 30048270
## ..$ bases : num [1:6] 5.48e+09 3.63e+09 3.72e+09 3.77e+09 5.48e+09 ...
## ..$ spots_with_mates : int [1:6] 53731689 35599757 36461836 36921253 53694963 30048270
## ..$ avgLength : int [1:6] 102 102 102 102 102 102
## ..$ size_MB : int [1:6] 3199 2124 2168 2190 3191 1757
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296133/SRR1296133.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296134/SRR1296134.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296135/SRR1296135.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296139/SRR1296139.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP042186" "SRP042186" "SRP042186" "SRP042186" ...
## ..$ BioProject : chr [1:6] "PRJNA248376" "PRJNA248376" "PRJNA248376" "PRJNA248376" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 248376 248376 248376 248376 248376 248376
## ..$ Sample : chr [1:6] "SRS618305" "SRS618306" "SRS618307" "SRS618311" ...
## ..$ BioSample : chr [1:6] "SAMN02798072" "SAMN02798080" "SAMN02798077" "SAMN02798084" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA166790" "SRA166790" "SRA166790" "SRA166790" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "ADCBB109469D3C7AA05EDA53049761C2" "D116BBF6679740971897ADBE7DB9E2FD" "5803894B2C76ECB37FA2AE4CD636FB48" "E0DAEB07BAFD462CFE6FB68CA77C46E1" ...
## ..$ ReadHash : chr [1:6] "0624C1859450C2507EE19A22D9FB3421" "0BA4D3A86930F2F334E786F373E9F1C0" "7A231A53FFC75AA3229F03A529D64DA2" "0237718B903CD918261E70CC51FEAC83" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP042186: Genes expressed differentially in human white vs brown adipose tissue with 24 hours of control treatment:White; SRX550549,SRX550550,SRX550551:Brown:SRX550561,SRX550562,SRX550563## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 3 variables:
## ..$ SRR1296118: int [1:58302] 1 12 2 1 0 0 0 0 0 1 ...
## ..$ SRR1296119: int [1:58302] 1 7 2 1 0 0 0 0 0 0 ...
## ..$ SRR1296120: int [1:58302] 0 15 4 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 3 variables:
## ..$ SRR1296118: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296119: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1296120: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 3 variables:
## ..$ SRR1296118: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296119: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR1296120: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 3 obs. of 7 variables:
## ..$ QC_summary : chr [1:3] "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:3] "SRX550549" "SRX550550" "SRX550551"
## ..$ SRS_accession: chr [1:3] "SRS618290" "SRS618291" "SRS618292"
## ..$ SRP_accession: chr [1:3] "SRP042186" "SRP042186" "SRP042186"
## ..$ Sample_name : chr [1:3] "GSM1396721" "GSM1396722" "GSM1396723"
## ..$ GEO_series : chr [1:3] "GSE57896" "GSE57896" "GSE57896"
## ..$ Library_name : logi [1:3] NA NA NA
## $ MetadataFull :'data.frame': 3 obs. of 52 variables:
## ..$ QC_summary : chr [1:3] "PASS" "PASS" "PASS"
## ..$ SRX_accession : chr [1:3] "SRX550549" "SRX550550" "SRX550551"
## ..$ SRS_accession : chr [1:3] "SRS618290" "SRS618291" "SRS618292"
## ..$ SRP_accession : chr [1:3] "SRP042186" "SRP042186" "SRP042186"
## ..$ Sample_name : chr [1:3] "GSM1396721" "GSM1396722" "GSM1396723"
## ..$ GEO_series : chr [1:3] "GSE57896" "GSE57896" "GSE57896"
## ..$ Library_name : logi [1:3] NA NA NA
## ..$ SampleName : chr [1:3] "GSM1396721" "GSM1396722" "GSM1396723"
## ..$ ReleaseDate : chr [1:3] "2014-11-03 08:58:11" "2014-11-03 08:58:11" "2014-11-03 08:58:11"
## ..$ LoadDate : chr [1:3] "2014-05-22 13:11:42" "2014-05-22 13:11:04" "2014-05-22 13:14:24"
## ..$ spots : int [1:3] 34149811 38262101 53895658
## ..$ bases : num [1:3] 3.48e+09 3.90e+09 5.50e+09
## ..$ spots_with_mates : int [1:3] 34149811 38262101 53895658
## ..$ avgLength : int [1:3] 102 102 102
## ..$ size_MB : int [1:3] 2044 2290 3234
## ..$ AssemblyName : logi [1:3] NA NA NA
## ..$ download_path : chr [1:3] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296118/SRR1296118.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296119/SRR1296119.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1296120/SRR1296120.1"
## ..$ LibraryName : logi [1:3] NA NA NA
## ..$ LibraryStrategy : chr [1:3] "RNA-Seq" "RNA-Seq" "RNA-Seq"
## ..$ LibrarySelection : chr [1:3] "cDNA" "cDNA" "cDNA"
## ..$ LibrarySource : chr [1:3] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr [1:3] "PAIRED" "PAIRED" "PAIRED"
## ..$ InsertSize : int [1:3] 0 0 0
## ..$ InsertDev : num [1:3] 0 0 0
## ..$ Platform : chr [1:3] "ILLUMINA" "ILLUMINA" "ILLUMINA"
## ..$ Model : chr [1:3] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000"
## ..$ SRAStudy : chr [1:3] "SRP042186" "SRP042186" "SRP042186"
## ..$ BioProject : chr [1:3] "PRJNA248376" "PRJNA248376" "PRJNA248376"
## ..$ Study_Pubmed_id : int [1:3] 2 2 2
## ..$ ProjectID : int [1:3] 248376 248376 248376
## ..$ Sample : chr [1:3] "SRS618290" "SRS618291" "SRS618292"
## ..$ BioSample : chr [1:3] "SAMN02798065" "SAMN02798067" "SAMN02798068"
## ..$ SampleType : chr [1:3] "simple" "simple" "simple"
## ..$ TaxID : int [1:3] 9606 9606 9606
## ..$ ScientificName : chr [1:3] "Homo sapiens" "Homo sapiens" "Homo sapiens"
## ..$ g1k_pop_code : logi [1:3] NA NA NA
## ..$ source : logi [1:3] NA NA NA
## ..$ g1k_analysis_group : logi [1:3] NA NA NA
## ..$ Subject_ID : logi [1:3] NA NA NA
## ..$ Sex : logi [1:3] NA NA NA
## ..$ Disease : logi [1:3] NA NA NA
## ..$ Tumor : chr [1:3] "no" "no" "no"
## ..$ Affection_Status : logi [1:3] NA NA NA
## ..$ Analyte_Type : logi [1:3] NA NA NA
## ..$ Histological_Type : logi [1:3] NA NA NA
## ..$ Body_Site : logi [1:3] NA NA NA
## ..$ CenterName : chr [1:3] "GEO" "GEO" "GEO"
## ..$ Submission : chr [1:3] "SRA166790" "SRA166790" "SRA166790"
## ..$ dbgap_study_accession: logi [1:3] NA NA NA
## ..$ Consent : chr [1:3] "public" "public" "public"
## ..$ RunHash : chr [1:3] "64458EB4A404CFB913E0646E670101BA" "985497D212662774B4BDE9859D1E28D0" "00D7C07EF1BC3B0AEE80A0A315FFF460"
## ..$ ReadHash : chr [1:3] "F255D6376DE2F3D6E4D706E80D975C21" "E8D27B4B5795AC99B2EDF5BA406A4AB3" "89E69D12D319BD0F21620C94848E4C84"
## $ absent : chr(0)## SRP045500: Genes expressed differentially in human neutrophils with type 1 diabetes:Ctrl; SRX680546,SRX680607,SRX680614,SRX680628:Diabetes; SRX680562,SRX680568,SRX680642,SRX680648
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR1550986: int [1:58302] 0 9 0 0 0 0 0 0 0 1 ...
## ..$ SRR1551002: int [1:58302] 1 38 1 0 0 0 0 0 0 1 ...
## ..$ SRR1551008: int [1:58302] 0 9 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551047: int [1:58302] 0 10 0 0 0 0 0 0 0 1 ...
## ..$ SRR1551054: int [1:58302] 0 17 1 0 0 0 0 0 0 5 ...
## ..$ SRR1551068: int [1:58302] 0 15 1 0 0 0 0 0 0 3 ...
## ..$ SRR1551082: int [1:58302] 0 5 0 0 0 0 0 0 0 2 ...
## ..$ SRR1551088: int [1:58302] 0 8 0 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR1550986: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551002: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551008: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551047: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551054: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551068: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551082: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551088: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR1550986: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551002: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551008: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551047: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551054: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551068: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551082: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551088: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "WARN(8)" "WARN(8)" "WARN(1,5,7,8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:8] "SRX680546" "SRX680562" "SRX680568" "SRX680607" ...
## ..$ SRS_accession: chr [1:8] "SRS684224" "SRS684241" "SRS684247" "SRS684286" ...
## ..$ SRP_accession: chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479438" "GSM1479454" "GSM1479460" "GSM1479499" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "WARN(8)" "WARN(8)" "WARN(1,5,7,8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:8] "SRX680546" "SRX680562" "SRX680568" "SRX680607" ...
## ..$ SRS_accession : chr [1:8] "SRS684224" "SRS684241" "SRS684247" "SRS684286" ...
## ..$ SRP_accession : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479438" "GSM1479454" "GSM1479460" "GSM1479499" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM1479438" "GSM1479454" "GSM1479460" "GSM1479499" ...
## ..$ ReleaseDate : chr [1:8] "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" ...
## ..$ LoadDate : chr [1:8] "2014-08-14 13:43:36" "2014-08-14 13:53:56" "2014-08-14 13:49:59" "2014-08-14 14:13:17" ...
## ..$ spots : int [1:8] 15170780 25300835 8840140 20264683 21299311 21014408 9978043 9991120
## ..$ bases : num [1:8] 1.52e+09 2.53e+09 8.84e+08 2.03e+09 2.13e+09 ...
## ..$ spots_with_mates : int [1:8] 15170780 25300835 8840140 20264683 21299311 21014408 9978043 9991120
## ..$ avgLength : int [1:8] 100 100 100 100 100 100 100 100
## ..$ size_MB : int [1:8] 834 1417 507 1273 1327 1312 611 607
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1550986/SRR1550986.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1551002/SRR1551002.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551008/SRR1551008.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551047/SRR1551047.1" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ BioProject : chr [1:8] "PRJNA258216" "PRJNA258216" "PRJNA258216" "PRJNA258216" ...
## ..$ Study_Pubmed_id : int [1:8] 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:8] 258216 258216 258216 258216 258216 258216 258216 258216
## ..$ Sample : chr [1:8] "SRS684224" "SRS684241" "SRS684247" "SRS684286" ...
## ..$ BioSample : chr [1:8] "SAMN02990322" "SAMN02990338" "SAMN02990344" "SAMN02990265" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA179316" "SRA179316" "SRA179316" "SRA179316" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "A4020653DDD5CACB7ED51471DE1904BC" "4ABD2DFB6B3DEDF4234DEF4B0DF505AB" "9CC32B2B7EA26E61EF2184BE7AEC7F2E" "E91F31EF960B9773A172C6D1D2920574" ...
## ..$ ReadHash : chr [1:8] "8AD4AFA89AC94FB7FF14E91764FF08C0" "29ABD731986A38D3AB2B8B1AC70C6D94" "C8761DD7AFF5ED1A370B985556D00791" "BE8E3177ADB2BDD32E3566E7241E7158" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP045500: Genes expressed differentially in human monocytes with type 1 diabetes:Ctrl; SRX680547,SRX680608,SRX680615,SRX680629:Diabetes; SRX680563,SRX680569,SRX680643,SRX680649## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR1550987: int [1:58302] 0 21 1 0 0 0 0 0 0 0 ...
## ..$ SRR1551003: int [1:58302] 0 48 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551009: int [1:58302] 0 29 1 0 0 0 0 0 0 0 ...
## ..$ SRR1551048: int [1:58302] 0 32 3 0 0 0 0 0 0 1 ...
## ..$ SRR1551055: int [1:58302] 0 21 4 0 0 0 0 0 0 0 ...
## ..$ SRR1551069: int [1:58302] 0 15 1 0 0 0 0 0 0 0 ...
## ..$ SRR1551083: int [1:58302] 0 15 1 0 0 0 0 0 0 0 ...
## ..$ SRR1551089: int [1:58302] 0 26 2 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR1550987: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551003: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551009: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551048: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551055: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551069: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551083: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551089: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR1550987: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551003: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551009: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551048: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551055: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551069: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551083: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551089: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:8] "SRX680547" "SRX680563" "SRX680569" "SRX680608" ...
## ..$ SRS_accession: chr [1:8] "SRS684227" "SRS684242" "SRS684248" "SRS684287" ...
## ..$ SRP_accession: chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479439" "GSM1479455" "GSM1479461" "GSM1479500" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:8] "SRX680547" "SRX680563" "SRX680569" "SRX680608" ...
## ..$ SRS_accession : chr [1:8] "SRS684227" "SRS684242" "SRS684248" "SRS684287" ...
## ..$ SRP_accession : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479439" "GSM1479455" "GSM1479461" "GSM1479500" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM1479439" "GSM1479455" "GSM1479461" "GSM1479500" ...
## ..$ ReleaseDate : chr [1:8] "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" ...
## ..$ LoadDate : chr [1:8] "2014-08-14 13:49:06" "2014-08-14 13:59:39" "2014-08-14 13:57:01" "2014-08-14 14:11:39" ...
## ..$ spots : int [1:8] 17740657 23069524 18301766 18451941 17419429 15968441 18133116 13135943
## ..$ bases : num [1:8] 1.77e+09 2.31e+09 1.83e+09 1.85e+09 1.74e+09 ...
## ..$ spots_with_mates : int [1:8] 17740657 23069524 18301766 18451941 17419429 15968441 18133116 13135943
## ..$ avgLength : int [1:8] 100 100 100 100 100 100 100 100
## ..$ size_MB : int [1:8] 991 1312 1024 1147 1080 998 1092 817
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1550987/SRR1550987.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551003/SRR1551003.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551009/SRR1551009.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1551048/SRR1551048.1" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ BioProject : chr [1:8] "PRJNA258216" "PRJNA258216" "PRJNA258216" "PRJNA258216" ...
## ..$ Study_Pubmed_id : int [1:8] 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:8] 258216 258216 258216 258216 258216 258216 258216 258216
## ..$ Sample : chr [1:8] "SRS684227" "SRS684242" "SRS684248" "SRS684287" ...
## ..$ BioSample : chr [1:8] "SAMN02990323" "SAMN02990339" "SAMN02990287" "SAMN02990266" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA179316" "SRA179316" "SRA179316" "SRA179316" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "CDD73CC75972A3582B215A0BA60FC816" "CB151AFFAAB93CD9DF10105BFD7A8AB2" "D403DC7252BC314DCF62678FD3FCB006" "61F423AF67512EEFEB7525FAFBF0474E" ...
## ..$ ReadHash : chr [1:8] "959B8EC8439F8A7E8AD9A7E1E85C5E55" "9FA8EC16611DF0BC76782ABFB84AEAF7" "7A66016FF7A909C4B95689249DDCDCD5" "292F6C5685B8084885B716609F222299" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP045500:Genes expressed differentially in human B-cells with type 1 diabetes:Ctrl; SRX680548,SRX680609,SRX680616,SRX680630:Diabetes; SRX680564,SRX680570,SRX680644,SRX680650## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR1550988: int [1:58302] 0 20 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551004: int [1:58302] 0 50 3 0 0 0 0 0 0 0 ...
## ..$ SRR1551010: int [1:58302] 1 37 4 0 0 0 0 0 0 0 ...
## ..$ SRR1551049: int [1:58302] 0 45 2 0 0 0 0 0 0 0 ...
## ..$ SRR1551056: int [1:58302] 0 63 3 0 0 0 0 0 0 0 ...
## ..$ SRR1551070: int [1:58302] 0 32 1 0 0 0 0 0 0 0 ...
## ..$ SRR1551084: int [1:58302] 1 54 7 2 0 0 0 0 0 1 ...
## ..$ SRR1551090: int [1:58302] 0 11 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR1550988: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551004: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551010: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551049: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551056: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551070: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551084: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551090: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR1550988: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551004: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551010: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551049: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551056: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551070: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551084: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551090: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:8] "SRX680548" "SRX680564" "SRX680570" "SRX680609" ...
## ..$ SRS_accession: chr [1:8] "SRS684226" "SRS684243" "SRS684249" "SRS684288" ...
## ..$ SRP_accession: chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479440" "GSM1479456" "GSM1479462" "GSM1479501" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:8] "SRX680548" "SRX680564" "SRX680570" "SRX680609" ...
## ..$ SRS_accession : chr [1:8] "SRS684226" "SRS684243" "SRS684249" "SRS684288" ...
## ..$ SRP_accession : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479440" "GSM1479456" "GSM1479462" "GSM1479501" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM1479440" "GSM1479456" "GSM1479462" "GSM1479501" ...
## ..$ ReleaseDate : chr [1:8] "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" ...
## ..$ LoadDate : chr [1:8] "2014-08-14 13:52:45" "2014-08-14 13:56:12" "2014-08-14 13:55:27" "2014-08-14 14:13:06" ...
## ..$ spots : int [1:8] 18985188 19257959 14955212 19455550 29182181 19528542 39528624 10256394
## ..$ bases : num [1:8] 1.90e+09 1.93e+09 1.50e+09 1.95e+09 2.92e+09 ...
## ..$ spots_with_mates : int [1:8] 18985188 19257959 14955212 19455550 29182181 19528542 39528624 10256394
## ..$ avgLength : int [1:8] 100 100 100 100 100 100 100 100
## ..$ size_MB : int [1:8] 1035 1075 850 1213 1843 1198 2378 633
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1550988/SRR1550988.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551004/SRR1551004.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551010/SRR1551010.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551049/SRR1551049.1" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ BioProject : chr [1:8] "PRJNA258216" "PRJNA258216" "PRJNA258216" "PRJNA258216" ...
## ..$ Study_Pubmed_id : int [1:8] 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:8] 258216 258216 258216 258216 258216 258216 258216 258216
## ..$ Sample : chr [1:8] "SRS684226" "SRS684243" "SRS684249" "SRS684288" ...
## ..$ BioSample : chr [1:8] "SAMN02990324" "SAMN02990340" "SAMN02990288" "SAMN02990270" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA179316" "SRA179316" "SRA179316" "SRA179316" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "68F89ECA2F2558A761782447176AC8DF" "1F9760A8B7E6F614B893F4E60767CFF7" "EC664F88C3637C84E31B27B39C21F0AF" "2BB4F07FA352F85CB7FD6177AF931F56" ...
## ..$ ReadHash : chr [1:8] "D02665357785785B41ECC73ADF82FD90" "873BA98D58A81416E5035D10D783F3B1" "F0DD3BBB91F6B71BBC8E5FC686284D23" "6B1DF61D055A5998C05E4EB7F7002828" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP045500:Genes expressed differentially in human CD4 with type 1 diabetes:Ctrl; SRX680549,SRX680610,SRX680617,SRX680631:Diabetes; SRX680565,SRX680571,SRX680645,SRX680651## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR1550989: int [1:58302] 0 18 1 0 0 0 0 0 0 0 ...
## ..$ SRR1551005: int [1:58302] 0 81 2 0 0 0 0 0 0 3 ...
## ..$ SRR1551011: int [1:58302] 0 41 6 1 0 0 0 0 0 2 ...
## ..$ SRR1551050: int [1:58302] 0 63 7 0 0 0 0 0 0 0 ...
## ..$ SRR1551057: int [1:58302] 0 55 3 0 0 0 0 0 0 0 ...
## ..$ SRR1551071: int [1:58302] 0 21 4 1 0 0 0 0 0 0 ...
## ..$ SRR1551085: int [1:58302] 0 20 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551091: int [1:58302] 0 25 4 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR1550989: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551005: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551011: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551050: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551057: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551071: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551085: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551091: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR1550989: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551005: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551011: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551050: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551057: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551071: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551085: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551091: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "PASS" "PASS" "WARN(5)" "PASS" ...
## ..$ SRX_accession: chr [1:8] "SRX680549" "SRX680565" "SRX680571" "SRX680610" ...
## ..$ SRS_accession: chr [1:8] "SRS684228" "SRS684245" "SRS684251" "SRS684289" ...
## ..$ SRP_accession: chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479441" "GSM1479457" "GSM1479463" "GSM1479502" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "PASS" "PASS" "WARN(5)" "PASS" ...
## ..$ SRX_accession : chr [1:8] "SRX680549" "SRX680565" "SRX680571" "SRX680610" ...
## ..$ SRS_accession : chr [1:8] "SRS684228" "SRS684245" "SRS684251" "SRS684289" ...
## ..$ SRP_accession : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479441" "GSM1479457" "GSM1479463" "GSM1479502" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM1479441" "GSM1479457" "GSM1479463" "GSM1479502" ...
## ..$ ReleaseDate : chr [1:8] "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" ...
## ..$ LoadDate : chr [1:8] "2014-08-14 13:47:42" "2014-08-14 13:58:07" "2014-08-14 13:57:31" "2014-08-14 14:16:27" ...
## ..$ spots : int [1:8] 15752774 25173451 14745620 25428087 21293876 19098826 8220738 7872484
## ..$ bases : num [1:8] 1.58e+09 2.52e+09 1.47e+09 2.54e+09 2.13e+09 ...
## ..$ spots_with_mates : int [1:8] 15752774 25173451 14745620 25428087 21293876 19098826 8220738 7872484
## ..$ avgLength : int [1:8] 100 100 100 100 100 100 100 100
## ..$ size_MB : int [1:8] 879 1423 813 1603 1327 1182 497 475
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1550989/SRR1550989.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551005/SRR1551005.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551011/SRR1551011.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551050/SRR1551050.1" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ BioProject : chr [1:8] "PRJNA258216" "PRJNA258216" "PRJNA258216" "PRJNA258216" ...
## ..$ Study_Pubmed_id : int [1:8] 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:8] 258216 258216 258216 258216 258216 258216 258216 258216
## ..$ Sample : chr [1:8] "SRS684228" "SRS684245" "SRS684251" "SRS684289" ...
## ..$ BioSample : chr [1:8] "SAMN02990325" "SAMN02990341" "SAMN02990289" "SAMN02990271" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA179316" "SRA179316" "SRA179316" "SRA179316" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "F22F0DC2BE6728ED740496D250BBAB9C" "95BD43EF0AD8AFB7FB4337ADEC9D7790" "69577D3E2EF4F9E4D7E6686EA7DFB46F" "760FD58C0E6B6A3D67CF8E25344D28CF" ...
## ..$ ReadHash : chr [1:8] "EA16F871ACDD8876A8FC9CFE5F8B16B3" "1B78961F3E2F1B05A64EEAFCEA042B77" "F77E8824222D400B965CADDEFDAC27C8" "DAD15CBE395C40F8509ABC149FB97B0F" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP045500:Genes expressed differentially in human CD8 with type 1 diabetes:Ctrl; SRX680550,SRX680611,SRX680618,SRX680632:Diabetes; SRX680566,SRX680572,SRX680646,SRX680652## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR1550990: int [1:58302] 0 26 4 0 0 0 0 0 0 0 ...
## ..$ SRR1551006: int [1:58302] 2 215 7 0 0 0 0 0 0 0 ...
## ..$ SRR1551012: int [1:58302] 0 37 3 0 0 0 0 0 0 0 ...
## ..$ SRR1551051: int [1:58302] 1 35 4 0 0 0 0 0 0 0 ...
## ..$ SRR1551058: int [1:58302] 0 45 4 0 0 0 0 0 0 0 ...
## ..$ SRR1551072: int [1:58302] 0 33 3 0 0 0 0 0 0 0 ...
## ..$ SRR1551086: int [1:58302] 0 52 1 0 0 0 0 0 0 0 ...
## ..$ SRR1551092: int [1:58302] 0 23 1 1 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR1550990: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551006: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551012: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551051: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551058: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551072: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551086: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551092: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR1550990: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551006: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551012: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551051: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551058: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551072: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551086: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551092: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "WARN(5)" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:8] "SRX680550" "SRX680566" "SRX680572" "SRX680611" ...
## ..$ SRS_accession: chr [1:8] "SRS684229" "SRS684244" "SRS684250" "SRS684290" ...
## ..$ SRP_accession: chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479442" "GSM1479458" "GSM1479464" "GSM1479503" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "WARN(5)" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:8] "SRX680550" "SRX680566" "SRX680572" "SRX680611" ...
## ..$ SRS_accession : chr [1:8] "SRS684229" "SRS684244" "SRS684250" "SRS684290" ...
## ..$ SRP_accession : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479442" "GSM1479458" "GSM1479464" "GSM1479503" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM1479442" "GSM1479458" "GSM1479464" "GSM1479503" ...
## ..$ ReleaseDate : chr [1:8] "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" ...
## ..$ LoadDate : chr [1:8] "2014-08-14 13:45:41" "2014-08-14 14:38:24" "2014-08-14 13:56:13" "2014-08-14 14:17:43" ...
## ..$ spots : int [1:8] 13394578 70578594 18434938 18241906 17816106 20997967 27271150 10473941
## ..$ bases : num [1:8] 1.34e+09 7.06e+09 1.84e+09 1.82e+09 1.78e+09 ...
## ..$ spots_with_mates : int [1:8] 13394578 70578594 18434938 18241906 17816106 20997967 27271150 10473941
## ..$ avgLength : int [1:8] 100 100 100 100 100 100 100 100
## ..$ size_MB : int [1:8] 736 4083 1042 1125 1108 1319 1684 633
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1550990/SRR1550990.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1551006/SRR1551006.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551012/SRR1551012.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551051/SRR1551051.1" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ BioProject : chr [1:8] "PRJNA258216" "PRJNA258216" "PRJNA258216" "PRJNA258216" ...
## ..$ Study_Pubmed_id : int [1:8] 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:8] 258216 258216 258216 258216 258216 258216 258216 258216
## ..$ Sample : chr [1:8] "SRS684229" "SRS684244" "SRS684250" "SRS684290" ...
## ..$ BioSample : chr [1:8] "SAMN02990331" "SAMN02990342" "SAMN02990290" "SAMN02990272" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA179316" "SRA179316" "SRA179316" "SRA179316" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "BA3B9359CA8C6A5481A68A79C025934D" "2118F2FAA8D100822CBE1C04DCC8DFB2" "FD5E3167D546C550599AD1EC8DD25B01" "A00EDF60DB08AE25A1220F6AEAEC107E" ...
## ..$ ReadHash : chr [1:8] "12954F1FB8A416A56D4F925726310131" "6D993AF1F7326888D40A47E1DC15B448" "A6EB590DE4EF127853E475099931129B" "F238DD1DA6C80D3120EEEECB494A58E6" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP045500:Genes expressed differentially in human NK with type 1 diabetes:Ctrl; SRX680551,SRX680612,SRX680619,SRX680633:Diabetes; SRX680567,SRX680653## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR1550991: int [1:58302] 0 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551007: int [1:58302] 0 34 2 0 0 0 0 0 0 0 ...
## ..$ SRR1551052: int [1:58302] 0 67 5 0 0 0 0 0 0 0 ...
## ..$ SRR1551059: int [1:58302] 0 43 4 0 0 0 0 0 0 0 ...
## ..$ SRR1551073: int [1:58302] 0 36 5 0 0 0 0 0 0 0 ...
## ..$ SRR1551093: int [1:58302] 0 18 3 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1550991: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551007: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551052: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551059: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551073: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551093: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR1550991: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551007: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551052: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551059: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551073: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551093: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(1,5,7)" "WARN(5,7)" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX680551" "SRX680567" "SRX680612" "SRX680619" ...
## ..$ SRS_accession: chr [1:6] "SRS684230" "SRS684246" "SRS684291" "SRS684298" ...
## ..$ SRP_accession: chr [1:6] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:6] "GSM1479443" "GSM1479459" "GSM1479504" "GSM1479511" ...
## ..$ GEO_series : chr [1:6] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(1,5,7)" "WARN(5,7)" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX680551" "SRX680567" "SRX680612" "SRX680619" ...
## ..$ SRS_accession : chr [1:6] "SRS684230" "SRS684246" "SRS684291" "SRS684298" ...
## ..$ SRP_accession : chr [1:6] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:6] "GSM1479443" "GSM1479459" "GSM1479504" "GSM1479511" ...
## ..$ GEO_series : chr [1:6] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1479443" "GSM1479459" "GSM1479504" "GSM1479511" ...
## ..$ ReleaseDate : chr [1:6] "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" ...
## ..$ LoadDate : chr [1:6] "2014-08-14 13:49:21" "2014-08-14 13:51:46" "2014-08-14 14:13:27" "2014-08-14 14:13:26" ...
## ..$ spots : int [1:6] 8983775 11845319 19287815 18547056 17882516 7812510
## ..$ bases : int [1:6] 898377500 1184531900 1928781500 1854705600 1788251600 781251000
## ..$ spots_with_mates : int [1:6] 8983775 11845319 19287815 18547056 17882516 7812510
## ..$ avgLength : int [1:6] 100 100 100 100 100 100
## ..$ size_MB : int [1:6] 514 671 1192 1147 1131 462
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1550991/SRR1550991.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551007/SRR1551007.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551052/SRR1551052.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1551059/SRR1551059.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:6] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ BioProject : chr [1:6] "PRJNA258216" "PRJNA258216" "PRJNA258216" "PRJNA258216" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 258216 258216 258216 258216 258216 258216
## ..$ Sample : chr [1:6] "SRS684230" "SRS684246" "SRS684291" "SRS684298" ...
## ..$ BioSample : chr [1:6] "SAMN02990332" "SAMN02990343" "SAMN02990273" "SAMN02990277" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA179316" "SRA179316" "SRA179316" "SRA179316" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "1D3F5DB9536F64B1C20A0DA3EA2F2640" "EFA465EE4A9934D8EBDFC135FB9A9370" "339BB28E4EDF8E80F21E1DD1CA284D11" "56A47B37F9B9643CAB8121D4DEFBE422" ...
## ..$ ReadHash : chr [1:6] "1C3D151F987B957EA273443A1C4593DE" "BFC28D8C66C57AD8E83A0B3DDBECF3BC" "9AE99BC46E79568FBBE22B1E37A32BC7" "9524C4AB9A2326AA9ACC85BC99E16E18" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP045500:Genes expressed differentially in human whole blood with type 1 diabetes:Ctrl;SRX680541,SRX680613,SRX680620,SRX680634:Diabetes; SRX680544,SRX680545,SRX680647,SRX680654## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR1550981: int [1:58302] 2 30 9 0 0 0 0 0 0 0 ...
## ..$ SRR1550984: int [1:58302] 0 44 4 0 0 0 0 0 0 0 ...
## ..$ SRR1550985: int [1:58302] 4 33 5 0 0 0 0 0 0 0 ...
## ..$ SRR1551053: int [1:58302] 1 45 5 0 0 0 0 0 0 0 ...
## ..$ SRR1551060: int [1:58302] 3 34 3 0 0 0 0 0 0 1 ...
## ..$ SRR1551074: int [1:58302] 0 14 3 1 0 0 0 0 0 0 ...
## ..$ SRR1551087: int [1:58302] 3 13 0 0 0 0 0 0 0 1 ...
## ..$ SRR1551094: int [1:58302] 5 86 8 1 0 0 0 0 0 4 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR1550981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1550984: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1550985: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551053: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551060: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551074: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551087: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1551094: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR1550981: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1550984: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1550985: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551053: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551060: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551074: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551087: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1551094: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:8] "SRX680541" "SRX680544" "SRX680545" "SRX680613" ...
## ..$ SRS_accession: chr [1:8] "SRS684220" "SRS684223" "SRS684225" "SRS684292" ...
## ..$ SRP_accession: chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479433" "GSM1479436" "GSM1479437" "GSM1479505" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:8] "SRX680541" "SRX680544" "SRX680545" "SRX680613" ...
## ..$ SRS_accession : chr [1:8] "SRS684220" "SRS684223" "SRS684225" "SRS684292" ...
## ..$ SRP_accession : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ Sample_name : chr [1:8] "GSM1479433" "GSM1479436" "GSM1479437" "GSM1479505" ...
## ..$ GEO_series : chr [1:8] "GSE60424" "GSE60424" "GSE60424" "GSE60424" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM1479433" "GSM1479436" "GSM1479437" "GSM1479505" ...
## ..$ ReleaseDate : chr [1:8] "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" "2015-01-07 16:59:14" ...
## ..$ LoadDate : chr [1:8] "2014-08-14 13:48:58" "2014-08-14 13:49:05" "2014-08-14 13:48:53" "2014-08-14 14:13:47" ...
## ..$ spots : int [1:8] 21878596 20602186 17899803 20596601 19237380 20839150 7405532 28091486
## ..$ bases : num [1:8] 2.19e+09 2.06e+09 1.79e+09 2.06e+09 1.92e+09 ...
## ..$ spots_with_mates : int [1:8] 21878596 20602186 17899803 20596601 19237380 20839150 7405532 28091486
## ..$ avgLength : int [1:8] 100 100 100 100 100 100 100 100
## ..$ size_MB : int [1:8] 1230 1172 979 1288 1194 1292 460 1740
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1550981/SRR1550981.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1550984/SRR1550984.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1550985/SRR1550985.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1551053/SRR1551053.1" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:8] "SRP045500" "SRP045500" "SRP045500" "SRP045500" ...
## ..$ BioProject : chr [1:8] "PRJNA258216" "PRJNA258216" "PRJNA258216" "PRJNA258216" ...
## ..$ Study_Pubmed_id : int [1:8] 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:8] 258216 258216 258216 258216 258216 258216 258216 258216
## ..$ Sample : chr [1:8] "SRS684220" "SRS684223" "SRS684225" "SRS684292" ...
## ..$ BioSample : chr [1:8] "SAMN02990317" "SAMN02990320" "SAMN02990321" "SAMN02990274" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA179316" "SRA179316" "SRA179316" "SRA179316" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "4B99132CE1CD8DAFF4574F0D06B92708" "57B98D7246DE2D80F5EB2C074F544645" "970E1E8BD6FD5BEB01C954446D2020FC" "70D24ED7A04799C64CB3A5D7DC984BF7" ...
## ..$ ReadHash : chr [1:8] "7407675138FA9BE7C73C326528CDB292" "BD72FFEF18F784EA5861C6B0AA879924" "50A5C59B1FC376E5F66D9F3ADF982655" "E0F9016447CF419C5062F617D99DDFE3" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP056835:Genes expressed differentially in human pancreatic alpha and beta cells:Alpha; SRX977631,SRX977632,SRX977633, SRX977634,SRX977635,SRX977636,SRX977637,SRX977638,SRX977639,SRX977640,SRX977641:Beta; SRX977624,SRX977625,SRX977626,SRX977627,SRX977628,SRX977629,SRX977630,SRX977642,SRX977643,SRX977644,SRX977645,SRX977646,SRX977647## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 24 variables:
## ..$ SRR1951541: int [1:58302] 0 3 2 0 0 0 0 0 1 1 ...
## ..$ SRR1951542: int [1:58302] 0 6 1 0 0 0 0 0 0 0 ...
## ..$ SRR1951543: int [1:58302] 0 10 2 0 0 0 0 0 0 0 ...
## ..$ SRR1951544: int [1:58302] 0 10 1 0 0 0 0 0 1 1 ...
## ..$ SRR1951545: int [1:58302] 0 16 0 0 0 0 1 0 0 0 ...
## ..$ SRR1951546: int [1:58302] 0 16 4 0 0 0 0 0 0 3 ...
## ..$ SRR1951547: int [1:58302] 0 9 1 0 0 0 0 0 0 0 ...
## ..$ SRR1951548: int [1:58302] 0 2 0 0 0 0 0 3 1 2 ...
## ..$ SRR1951549: int [1:58302] 1 7 0 0 0 0 0 1 0 2 ...
## ..$ SRR1951550: int [1:58302] 0 3 2 0 0 0 0 2 2 0 ...
## ..$ SRR1951551: int [1:58302] 0 9 2 0 0 0 0 0 0 2 ...
## ..$ SRR1951552: int [1:58302] 0 10 0 0 0 0 3 0 1 5 ...
## ..$ SRR1951553: int [1:58302] 1 20 3 0 0 0 0 2 3 1 ...
## ..$ SRR1951554: int [1:58302] 0 14 4 0 0 1 0 0 0 42 ...
## ..$ SRR1951555: int [1:58302] 0 14 9 0 0 0 0 0 0 5 ...
## ..$ SRR1951556: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951557: int [1:58302] 0 11 0 0 0 0 0 0 0 5 ...
## ..$ SRR1951558: int [1:58302] 0 1 0 0 0 0 0 0 0 2 ...
## ..$ SRR1951559: int [1:58302] 0 4 0 0 0 0 0 0 0 16 ...
## ..$ SRR1951560: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR1951561: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951562: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951563: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951564: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 24 variables:
## ..$ SRR1951541: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951542: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951543: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951544: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951545: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951546: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951547: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951548: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951549: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951550: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951551: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951552: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951553: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951554: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951555: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951556: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951557: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951558: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951559: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951560: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951561: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951562: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951563: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951564: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 24 variables:
## ..$ SRR1951541: chr [1:30] "PE" "Sanger/Illumina1.9" "90" "90" ...
## ..$ SRR1951542: chr [1:30] "PE" "Sanger/Illumina1.9" "90" "90" ...
## ..$ SRR1951543: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951544: chr [1:30] "PE" "Sanger/Illumina1.9" "90" "90" ...
## ..$ SRR1951545: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951546: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951547: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951548: chr [1:30] "PE" "Sanger/Illumina1.9" "90" "90" ...
## ..$ SRR1951549: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951550: chr [1:30] "PE" "Sanger/Illumina1.9" "90" "90" ...
## ..$ SRR1951551: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951552: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951553: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951554: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951555: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951556: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951557: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951558: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951559: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR1951560: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR1951561: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR1951562: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR1951563: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR1951564: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## $ MetadataSummary:'data.frame': 24 obs. of 7 variables:
## ..$ QC_summary : chr [1:24] "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(2)" "FAIL(4,6)" ...
## ..$ SRX_accession: chr [1:24] "SRX977624" "SRX977625" "SRX977626" "SRX977627" ...
## ..$ SRS_accession: chr [1:24] "SRS892662" "SRS892663" "SRS892661" "SRS892660" ...
## ..$ SRP_accession: chr [1:24] "SRP056835" "SRP056835" "SRP056835" "SRP056835" ...
## ..$ Sample_name : chr [1:24] "GSM1649191" "GSM1649192" "GSM1649193" "GSM1649194" ...
## ..$ GEO_series : chr [1:24] "GSE67543" "GSE67543" "GSE67543" "GSE67543" ...
## ..$ Library_name : logi [1:24] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 24 obs. of 52 variables:
## ..$ QC_summary : chr [1:24] "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(2)" "FAIL(4,6)" ...
## ..$ SRX_accession : chr [1:24] "SRX977624" "SRX977625" "SRX977626" "SRX977627" ...
## ..$ SRS_accession : chr [1:24] "SRS892662" "SRS892663" "SRS892661" "SRS892660" ...
## ..$ SRP_accession : chr [1:24] "SRP056835" "SRP056835" "SRP056835" "SRP056835" ...
## ..$ Sample_name : chr [1:24] "GSM1649191" "GSM1649192" "GSM1649193" "GSM1649194" ...
## ..$ GEO_series : chr [1:24] "GSE67543" "GSE67543" "GSE67543" "GSE67543" ...
## ..$ Library_name : logi [1:24] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:24] "GSM1649191" "GSM1649192" "GSM1649193" "GSM1649194" ...
## ..$ ReleaseDate : chr [1:24] "2015-06-09 16:48:28" "2015-06-09 16:48:28" "2015-06-09 16:48:28" "2015-06-09 16:48:28" ...
## ..$ LoadDate : chr [1:24] "2015-04-02 17:26:17" "2015-04-02 17:21:09" "2015-04-02 17:22:52" "2015-04-02 17:14:20" ...
## ..$ spots : int [1:24] 39751075 39135814 38003513 13766302 34767865 41468118 35479915 42364056 40077602 41991390 ...
## ..$ bases : num [1:24] 7.16e+09 7.04e+09 7.60e+09 2.48e+09 6.95e+09 ...
## ..$ spots_with_mates : int [1:24] 39751075 39135814 38003513 13766302 34767865 41468118 35479915 42364056 40077602 41991390 ...
## ..$ avgLength : int [1:24] 180 180 200 180 200 200 200 180 200 180 ...
## ..$ size_MB : int [1:24] 5011 4927 5203 1610 4777 5713 4845 5307 5520 5232 ...
## ..$ AssemblyName : logi [1:24] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:24] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1951541/SRR1951541.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1951542/SRR1951542.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1951543/SRR1951543.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1951544/SRR1951544.1" ...
## ..$ LibraryName : logi [1:24] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:24] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:24] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:24] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:24] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:24] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:24] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:24] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:24] "SRP056835" "SRP056835" "SRP056835" "SRP056835" ...
## ..$ BioProject : chr [1:24] "PRJNA280220" "PRJNA280220" "PRJNA280220" "PRJNA280220" ...
## ..$ Study_Pubmed_id : int [1:24] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:24] 280220 280220 280220 280220 280220 280220 280220 280220 280220 280220 ...
## ..$ Sample : chr [1:24] "SRS892662" "SRS892663" "SRS892661" "SRS892660" ...
## ..$ BioSample : chr [1:24] "SAMN03458661" "SAMN03458662" "SAMN03458663" "SAMN03458664" ...
## ..$ SampleType : chr [1:24] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:24] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:24] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:24] NA NA NA NA NA NA ...
## ..$ source : logi [1:24] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:24] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:24] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:24] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:24] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:24] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:24] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:24] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:24] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:24] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:24] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:24] "SRA249768" "SRA249768" "SRA249768" "SRA249768" ...
## ..$ dbgap_study_accession: logi [1:24] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:24] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:24] "6261EC17C2B716EA36B8904E53BF867F" "6EB49E17028C15B6FF5CDD4E4786C939" "6CF37E8F7652C6FEB26B8662C2D6884E" "178B54E3B437070B538E0B01829DADB7" ...
## ..$ ReadHash : chr [1:24] "ABD08C43B78A55420C2B72E396526EAC" "74D0A7AB0474F299D1E70E95E52E4A64" "212AE6F56A8E0B093E9096B934C8E72C" "28D017A43CAC941829CFA4E77B8DAB0A" ...
## $ absent : chr(0)## SRP056835:Genes expressed differentially in human pancreatic adult and fetal cells:Adult; SRX977624,SRX977625,SRX977626, SRX977627,SRX977628,SRX977629,SRX977630,SRX977631,SRX977632,SRX977633,SRX977634,SRX977635,SRX977636:Fetal; SRX977637,SRX977638,SRX977639,SRX9776340,SRX977641,SRX977642,SRX977643,SRX977644,SRX977645,SRX977646,SRX977647
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 23 variables:
## ..$ SRR1951541: int [1:58302] 0 3 2 0 0 0 0 0 1 1 ...
## ..$ SRR1951542: int [1:58302] 0 6 1 0 0 0 0 0 0 0 ...
## ..$ SRR1951543: int [1:58302] 0 10 2 0 0 0 0 0 0 0 ...
## ..$ SRR1951544: int [1:58302] 0 10 1 0 0 0 0 0 1 1 ...
## ..$ SRR1951545: int [1:58302] 0 16 0 0 0 0 1 0 0 0 ...
## ..$ SRR1951546: int [1:58302] 0 16 4 0 0 0 0 0 0 3 ...
## ..$ SRR1951547: int [1:58302] 0 9 1 0 0 0 0 0 0 0 ...
## ..$ SRR1951548: int [1:58302] 0 2 0 0 0 0 0 3 1 2 ...
## ..$ SRR1951549: int [1:58302] 1 7 0 0 0 0 0 1 0 2 ...
## ..$ SRR1951550: int [1:58302] 0 3 2 0 0 0 0 2 2 0 ...
## ..$ SRR1951551: int [1:58302] 0 9 2 0 0 0 0 0 0 2 ...
## ..$ SRR1951552: int [1:58302] 0 10 0 0 0 0 3 0 1 5 ...
## ..$ SRR1951553: int [1:58302] 1 20 3 0 0 0 0 2 3 1 ...
## ..$ SRR1951554: int [1:58302] 0 14 4 0 0 1 0 0 0 42 ...
## ..$ SRR1951555: int [1:58302] 0 14 9 0 0 0 0 0 0 5 ...
## ..$ SRR1951556: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951558: int [1:58302] 0 1 0 0 0 0 0 0 0 2 ...
## ..$ SRR1951559: int [1:58302] 0 4 0 0 0 0 0 0 0 16 ...
## ..$ SRR1951560: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR1951561: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951562: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951563: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951564: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 23 variables:
## ..$ SRR1951541: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951542: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951543: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951544: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951545: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951546: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951547: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951548: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951549: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951550: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951551: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951552: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951553: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951554: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951555: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951556: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951558: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951559: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951560: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951561: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951562: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951563: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1951564: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 23 variables:
## ..$ SRR1951541: chr [1:30] "PE" "Sanger/Illumina1.9" "90" "90" ...
## ..$ SRR1951542: chr [1:30] "PE" "Sanger/Illumina1.9" "90" "90" ...
## ..$ SRR1951543: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951544: chr [1:30] "PE" "Sanger/Illumina1.9" "90" "90" ...
## ..$ SRR1951545: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951546: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951547: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951548: chr [1:30] "PE" "Sanger/Illumina1.9" "90" "90" ...
## ..$ SRR1951549: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951550: chr [1:30] "PE" "Sanger/Illumina1.9" "90" "90" ...
## ..$ SRR1951551: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951552: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951553: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951554: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951555: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951556: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951558: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR1951559: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR1951560: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR1951561: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR1951562: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR1951563: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR1951564: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## $ MetadataSummary:'data.frame': 23 obs. of 7 variables:
## ..$ QC_summary : chr [1:23] "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(2)" "FAIL(4,6)" ...
## ..$ SRX_accession: chr [1:23] "SRX977624" "SRX977625" "SRX977626" "SRX977627" ...
## ..$ SRS_accession: chr [1:23] "SRS892662" "SRS892663" "SRS892661" "SRS892660" ...
## ..$ SRP_accession: chr [1:23] "SRP056835" "SRP056835" "SRP056835" "SRP056835" ...
## ..$ Sample_name : chr [1:23] "GSM1649191" "GSM1649192" "GSM1649193" "GSM1649194" ...
## ..$ GEO_series : chr [1:23] "GSE67543" "GSE67543" "GSE67543" "GSE67543" ...
## ..$ Library_name : logi [1:23] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 23 obs. of 52 variables:
## ..$ QC_summary : chr [1:23] "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(2)" "FAIL(4,6)" ...
## ..$ SRX_accession : chr [1:23] "SRX977624" "SRX977625" "SRX977626" "SRX977627" ...
## ..$ SRS_accession : chr [1:23] "SRS892662" "SRS892663" "SRS892661" "SRS892660" ...
## ..$ SRP_accession : chr [1:23] "SRP056835" "SRP056835" "SRP056835" "SRP056835" ...
## ..$ Sample_name : chr [1:23] "GSM1649191" "GSM1649192" "GSM1649193" "GSM1649194" ...
## ..$ GEO_series : chr [1:23] "GSE67543" "GSE67543" "GSE67543" "GSE67543" ...
## ..$ Library_name : logi [1:23] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:23] "GSM1649191" "GSM1649192" "GSM1649193" "GSM1649194" ...
## ..$ ReleaseDate : chr [1:23] "2015-06-09 16:48:28" "2015-06-09 16:48:28" "2015-06-09 16:48:28" "2015-06-09 16:48:28" ...
## ..$ LoadDate : chr [1:23] "2015-04-02 17:26:17" "2015-04-02 17:21:09" "2015-04-02 17:22:52" "2015-04-02 17:14:20" ...
## ..$ spots : int [1:23] 39751075 39135814 38003513 13766302 34767865 41468118 35479915 42364056 40077602 41991390 ...
## ..$ bases : num [1:23] 7.16e+09 7.04e+09 7.60e+09 2.48e+09 6.95e+09 ...
## ..$ spots_with_mates : int [1:23] 39751075 39135814 38003513 13766302 34767865 41468118 35479915 42364056 40077602 41991390 ...
## ..$ avgLength : int [1:23] 180 180 200 180 200 200 200 180 200 180 ...
## ..$ size_MB : int [1:23] 5011 4927 5203 1610 4777 5713 4845 5307 5520 5232 ...
## ..$ AssemblyName : logi [1:23] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:23] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1951541/SRR1951541.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1951542/SRR1951542.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1951543/SRR1951543.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1951544/SRR1951544.1" ...
## ..$ LibraryName : logi [1:23] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:23] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:23] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:23] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:23] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:23] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:23] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:23] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:23] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:23] "SRP056835" "SRP056835" "SRP056835" "SRP056835" ...
## ..$ BioProject : chr [1:23] "PRJNA280220" "PRJNA280220" "PRJNA280220" "PRJNA280220" ...
## ..$ Study_Pubmed_id : int [1:23] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:23] 280220 280220 280220 280220 280220 280220 280220 280220 280220 280220 ...
## ..$ Sample : chr [1:23] "SRS892662" "SRS892663" "SRS892661" "SRS892660" ...
## ..$ BioSample : chr [1:23] "SAMN03458661" "SAMN03458662" "SAMN03458663" "SAMN03458664" ...
## ..$ SampleType : chr [1:23] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:23] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:23] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:23] NA NA NA NA NA NA ...
## ..$ source : logi [1:23] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:23] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:23] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:23] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:23] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:23] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:23] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:23] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:23] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:23] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:23] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:23] "SRA249768" "SRA249768" "SRA249768" "SRA249768" ...
## ..$ dbgap_study_accession: logi [1:23] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:23] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:23] "6261EC17C2B716EA36B8904E53BF867F" "6EB49E17028C15B6FF5CDD4E4786C939" "6CF37E8F7652C6FEB26B8662C2D6884E" "178B54E3B437070B538E0B01829DADB7" ...
## ..$ ReadHash : chr [1:23] "ABD08C43B78A55420C2B72E396526EAC" "74D0A7AB0474F299D1E70E95E52E4A64" "212AE6F56A8E0B093E9096B934C8E72C" "28D017A43CAC941829CFA4E77B8DAB0A" ...
## $ absent : chr(0)## SRP067701:Genes expressed differentially in glucagon-secreting α-cells and insulin-secreting β-cells:Alpha; SRX1497368,SRX1497369,SRX1497370,SRX1497371,SRX1497372,SRX1497373,SRX1497374:Beta; SRX1497375,SRX1497376,SRX1497377,SRX1497378,SRX1497379,SRX1497380,SRX1497381,SRX1497382
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 29 variables:
## ..$ SRR3048055: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR3048056: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR3048057: int [1:58302] 0 2 2 0 0 0 0 0 0 0 ...
## ..$ SRR3048058: int [1:58302] 1 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048059: int [1:58302] 8 23 6 0 0 0 0 16 0 2 ...
## ..$ SRR3048060: int [1:58302] 2 27 9 4 0 0 0 2 0 0 ...
## ..$ SRR3048061: int [1:58302] 0 5 2 0 0 0 0 0 0 1 ...
## ..$ SRR3048062: int [1:58302] 1 12 4 0 0 0 0 1 0 1 ...
## ..$ SRR3048063: int [1:58302] 3 17 3 0 0 0 0 0 0 2 ...
## ..$ SRR3048064: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR3048065: int [1:58302] 0 1 1 0 0 0 0 0 0 3 ...
## ..$ SRR3048066: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR3048067: int [1:58302] 0 0 0 0 0 0 2 5 0 1 ...
## ..$ SRR3048068: int [1:58302] 0 0 0 0 0 0 0 0 0 2 ...
## ..$ SRR3048069: int [1:58302] 0 1 0 1 0 0 2 0 0 0 ...
## ..$ SRR3048070: int [1:58302] 0 3 0 0 0 0 0 0 0 3 ...
## ..$ SRR3048071: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048072: int [1:58302] 1 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048073: int [1:58302] 1 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048074: int [1:58302] 19 1 2 0 0 0 0 10 2 17 ...
## ..$ SRR3048075: int [1:58302] 6 62 9 0 0 0 0 7 0 4 ...
## ..$ SRR3048076: int [1:58302] 2 10 9 2 0 0 0 2 0 0 ...
## ..$ SRR3048077: int [1:58302] 2 7 1 0 0 0 0 0 0 0 ...
## ..$ SRR3048078: int [1:58302] 0 10 1 0 0 0 0 0 1 0 ...
## ..$ SRR3048079: int [1:58302] 0 8 2 0 0 0 0 0 1 0 ...
## ..$ SRR3048080: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048081: int [1:58302] 0 0 0 0 0 0 0 0 1 0 ...
## ..$ SRR3048082: int [1:58302] 0 0 2 0 0 0 0 1 0 0 ...
## ..$ SRR3048083: int [1:58302] 0 3 5 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 29 variables:
## ..$ SRR3048055: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048056: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048057: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048058: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048059: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048060: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048061: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048062: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048063: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048064: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048065: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048066: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048067: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048068: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048069: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048070: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048071: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048072: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048073: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048074: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048075: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048076: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048077: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048078: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048079: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048080: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048081: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048082: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3048083: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 29 variables:
## ..$ SRR3048055: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048056: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048057: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048058: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048059: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048060: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048061: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048062: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048063: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048064: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048065: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048066: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048067: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048068: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048069: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048070: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048071: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048072: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048073: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048074: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048075: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048076: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048077: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048078: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048079: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048080: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048081: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048082: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3048083: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 29 obs. of 7 variables:
## ..$ QC_summary : chr [1:29] "WARN(8)" "WARN(5,7,8)" "WARN(5,8)" "WARN(5,8)" ...
## ..$ SRX_accession: chr [1:29] "SRX1497368" "SRX1497369" "SRX1497369" "SRX1497369" ...
## ..$ SRS_accession: chr [1:29] "SRS1219090" "SRS1219089" "SRS1219089" "SRS1219089" ...
## ..$ SRP_accession: chr [1:29] "SRP067701" "SRP067701" "SRP067701" "SRP067701" ...
## ..$ Sample_name : chr [1:29] "GSM1978251" "GSM1978252" "GSM1978252" "GSM1978252" ...
## ..$ GEO_series : chr [1:29] "GSE76268" "GSE76268" "GSE76268" "GSE76268" ...
## ..$ Library_name : logi [1:29] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 29 obs. of 52 variables:
## ..$ QC_summary : chr [1:29] "WARN(8)" "WARN(5,7,8)" "WARN(5,8)" "WARN(5,8)" ...
## ..$ SRX_accession : chr [1:29] "SRX1497368" "SRX1497369" "SRX1497369" "SRX1497369" ...
## ..$ SRS_accession : chr [1:29] "SRS1219090" "SRS1219089" "SRS1219089" "SRS1219089" ...
## ..$ SRP_accession : chr [1:29] "SRP067701" "SRP067701" "SRP067701" "SRP067701" ...
## ..$ Sample_name : chr [1:29] "GSM1978251" "GSM1978252" "GSM1978252" "GSM1978252" ...
## ..$ GEO_series : chr [1:29] "GSE76268" "GSE76268" "GSE76268" "GSE76268" ...
## ..$ Library_name : logi [1:29] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:29] "GSM1978251" "GSM1978252" "GSM1978252" "GSM1978252" ...
## ..$ ReleaseDate : chr [1:29] "2015-12-27 19:52:05" "2015-12-27 19:52:05" "2015-12-27 19:52:05" "2015-12-27 19:52:05" ...
## ..$ LoadDate : chr [1:29] "2015-12-22 14:14:48" "2015-12-22 14:11:58" "2015-12-22 14:10:01" "2015-12-22 14:10:38" ...
## ..$ spots : int [1:29] 35792489 12495498 15691521 15681374 97704374 72405803 12246620 15279933 15249800 12027850 ...
## ..$ bases : num [1:29] 3.58e+09 1.25e+09 1.57e+09 1.57e+09 9.77e+09 ...
## ..$ spots_with_mates : int [1:29] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:29] 100 100 100 100 100 100 100 100 100 100 ...
## ..$ size_MB : int [1:29] 2256 811 979 979 5706 4102 793 952 951 776 ...
## ..$ AssemblyName : logi [1:29] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:29] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR3048055/SRR3048055.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR3048056/SRR3048056.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR3048057/SRR3048057.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR3048058/SRR3048058.1" ...
## ..$ LibraryName : logi [1:29] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:29] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:29] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:29] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:29] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:29] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:29] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:29] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:29] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:29] "SRP067701" "SRP067701" "SRP067701" "SRP067701" ...
## ..$ BioProject : chr [1:29] "PRJNA306754" "PRJNA306754" "PRJNA306754" "PRJNA306754" ...
## ..$ Study_Pubmed_id : int [1:29] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:29] 306754 306754 306754 306754 306754 306754 306754 306754 306754 306754 ...
## ..$ Sample : chr [1:29] "SRS1219090" "SRS1219089" "SRS1219089" "SRS1219089" ...
## ..$ BioSample : chr [1:29] "SAMN04362230" "SAMN04362216" "SAMN04362216" "SAMN04362216" ...
## ..$ SampleType : chr [1:29] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:29] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:29] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:29] NA NA NA NA NA NA ...
## ..$ source : logi [1:29] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:29] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:29] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:29] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:29] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:29] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:29] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:29] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:29] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:29] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:29] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:29] "SRA321280" "SRA321280" "SRA321280" "SRA321280" ...
## ..$ dbgap_study_accession: logi [1:29] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:29] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:29] "3168030E7CFD426BCA078655098DEDCB" "347350FD411045D793093B4FF57A5918" "A4B16F61F19643646A5DEDC8D1870855" "933561861879D92ED8A1A141DEDE2207" ...
## ..$ ReadHash : chr [1:29] "054B92ACBF516AACAC060E56B54ECF26" "3B33DE28F28B002E8DF31FCF5E9050DE" "B2DC453ACA67D6A40113A1F1039D2235" "E4CC80AFB13AA0489208F935783E5357" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP068733:Genes expressed differentially in diabetic endothelial cells treated with SAHA:Ctrl; SRX1540354,SRX1540355,SRX1540356:SAHA; SRX1540357,SRX1540358,SRX1540359## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR3112222: int [1:58302] 0 0 2 0 0 0 0 0 0 1 ...
## ..$ SRR3112223: int [1:58302] 0 0 5 0 0 0 0 0 0 0 ...
## ..$ SRR3112224: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR3112225: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112226: int [1:58302] 0 1 5 0 0 0 0 0 0 0 ...
## ..$ SRR3112227: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR3112222: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112223: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112224: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112225: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112226: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112227: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR3112222: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112223: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112224: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112225: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112226: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112227: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX1540354" "SRX1540355" "SRX1540356" "SRX1540357" ...
## ..$ SRS_accession: chr [1:6] "SRS1256809" "SRS1256808" "SRS1256807" "SRS1256806" ...
## ..$ SRP_accession: chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:6] "GSM2044434" "GSM2044435" "GSM2044436" "GSM2044437" ...
## ..$ GEO_series : chr [1:6] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX1540354" "SRX1540355" "SRX1540356" "SRX1540357" ...
## ..$ SRS_accession : chr [1:6] "SRS1256809" "SRS1256808" "SRS1256807" "SRS1256806" ...
## ..$ SRP_accession : chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:6] "GSM2044434" "GSM2044435" "GSM2044436" "GSM2044437" ...
## ..$ GEO_series : chr [1:6] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2044434" "GSM2044435" "GSM2044436" "GSM2044437" ...
## ..$ ReleaseDate : chr [1:6] "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" ...
## ..$ LoadDate : chr [1:6] "2016-01-21 18:56:26" "2016-01-21 18:55:15" "2016-01-21 18:54:36" "2016-01-21 18:54:33" ...
## ..$ spots : int [1:6] 29127539 25319531 23007303 24422294 19832359 21887841
## ..$ bases : num [1:6] 2.91e+09 2.53e+09 2.30e+09 2.44e+09 1.98e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 100 100 100 100 100 100
## ..$ size_MB : int [1:6] 1207 1048 976 1016 834 930
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112222/SRR3112222.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112223/SRR3112223.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112224/SRR3112224.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112225/SRR3112225.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ BioProject : chr [1:6] "PRJNA309443" "PRJNA309443" "PRJNA309443" "PRJNA309443" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 309443 309443 309443 309443 309443 309443
## ..$ Sample : chr [1:6] "SRS1256809" "SRS1256808" "SRS1256807" "SRS1256806" ...
## ..$ BioSample : chr [1:6] "SAMN04433002" "SAMN04433003" "SAMN04433004" "SAMN04433005" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA337501" "SRA337501" "SRA337501" "SRA337501" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "F30DCB326FF5E049FCE351CBD262C40E" "A329F0AA3F3FBF4DF1A6F6CBE1F86A61" "F3DD148FA2EF06D1ECD973ED930D660C" "4FC1B69249158E432354AE5FA775B301" ...
## ..$ ReadHash : chr [1:6] "88EA0F43E25F8BA3B3D92F85F59BF097" "B4EF544E9879FECCA82D276CE6032DC0" "120CACB855B17F9618686C6AD220EE62" "7495E725EE0D091BC9EC81E7D052EEC7" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP068733:Genes expressed differentially in diabetic endothelial cells treated with C646:Ctrl; SRX1540354,SRX1540355,SRX1540356:C646;SRX1540360,SRX1540361,SRX1540362## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR3112222: int [1:58302] 0 0 2 0 0 0 0 0 0 1 ...
## ..$ SRR3112223: int [1:58302] 0 0 5 0 0 0 0 0 0 0 ...
## ..$ SRR3112224: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR3112229: int [1:58302] 0 1 2 0 0 0 0 0 0 1 ...
## ..$ SRR3112230: int [1:58302] 0 0 1 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR3112222: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112223: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112224: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112229: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112230: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR3112222: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112223: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112224: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112229: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112230: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "PASS" "PASS" "PASS" "WARN(8)" ...
## ..$ SRX_accession: chr [1:5] "SRX1540354" "SRX1540355" "SRX1540356" "SRX1540361" ...
## ..$ SRS_accession: chr [1:5] "SRS1256809" "SRS1256808" "SRS1256807" "SRS1256802" ...
## ..$ SRP_accession: chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:5] "GSM2044434" "GSM2044435" "GSM2044436" "GSM2044441" ...
## ..$ GEO_series : chr [1:5] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "PASS" "PASS" "PASS" "WARN(8)" ...
## ..$ SRX_accession : chr [1:5] "SRX1540354" "SRX1540355" "SRX1540356" "SRX1540361" ...
## ..$ SRS_accession : chr [1:5] "SRS1256809" "SRS1256808" "SRS1256807" "SRS1256802" ...
## ..$ SRP_accession : chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:5] "GSM2044434" "GSM2044435" "GSM2044436" "GSM2044441" ...
## ..$ GEO_series : chr [1:5] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM2044434" "GSM2044435" "GSM2044436" "GSM2044441" ...
## ..$ ReleaseDate : chr [1:5] "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" ...
## ..$ LoadDate : chr [1:5] "2016-01-21 18:56:26" "2016-01-21 18:55:15" "2016-01-21 18:54:36" "2016-01-21 18:55:37" ...
## ..$ spots : int [1:5] 29127539 25319531 23007303 24717466 21028011
## ..$ bases : num [1:5] 2.91e+09 2.53e+09 2.30e+09 2.47e+09 2.10e+09
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 100 100 100 100 100
## ..$ size_MB : int [1:5] 1207 1048 976 1037 892
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112222/SRR3112222.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112223/SRR3112223.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112224/SRR3112224.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112229/SRR3112229.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ BioProject : chr [1:5] "PRJNA309443" "PRJNA309443" "PRJNA309443" "PRJNA309443" ...
## ..$ Study_Pubmed_id : int [1:5] 2 2 2 2 2
## ..$ ProjectID : int [1:5] 309443 309443 309443 309443 309443
## ..$ Sample : chr [1:5] "SRS1256809" "SRS1256808" "SRS1256807" "SRS1256802" ...
## ..$ BioSample : chr [1:5] "SAMN04433002" "SAMN04433003" "SAMN04433004" "SAMN04433009" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA337501" "SRA337501" "SRA337501" "SRA337501" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "F30DCB326FF5E049FCE351CBD262C40E" "A329F0AA3F3FBF4DF1A6F6CBE1F86A61" "F3DD148FA2EF06D1ECD973ED930D660C" "D2625577AFA24FDD1A5663D94C4CB49A" ...
## ..$ ReadHash : chr [1:5] "88EA0F43E25F8BA3B3D92F85F59BF097" "B4EF544E9879FECCA82D276CE6032DC0" "120CACB855B17F9618686C6AD220EE62" "E97998F035677E4ECE4BEBB99C68449A" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP068733:Genes expressed differentially in diabetic endothelial cells treated with ep300 siRNA compared to diabetic cells treated with DMSO:Ctrl;SRX1540354,SRX1540355,SRX1540356:ep300siRNA;SRX1540366,SRX1540367,SRX1540368## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR3112222: int [1:58302] 0 0 2 0 0 0 0 0 0 1 ...
## ..$ SRR3112223: int [1:58302] 0 0 5 0 0 0 0 0 0 0 ...
## ..$ SRR3112224: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR3112234: int [1:58302] 0 1 6 0 0 0 0 0 0 0 ...
## ..$ SRR3112236: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR3112222: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112223: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112224: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112234: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112236: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR3112222: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112223: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112224: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112234: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112236: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:5] "SRX1540354" "SRX1540355" "SRX1540356" "SRX1540366" ...
## ..$ SRS_accession: chr [1:5] "SRS1256809" "SRS1256808" "SRS1256807" "SRS1256797" ...
## ..$ SRP_accession: chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:5] "GSM2044434" "GSM2044435" "GSM2044436" "GSM2044446" ...
## ..$ GEO_series : chr [1:5] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:5] "SRX1540354" "SRX1540355" "SRX1540356" "SRX1540366" ...
## ..$ SRS_accession : chr [1:5] "SRS1256809" "SRS1256808" "SRS1256807" "SRS1256797" ...
## ..$ SRP_accession : chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:5] "GSM2044434" "GSM2044435" "GSM2044436" "GSM2044446" ...
## ..$ GEO_series : chr [1:5] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM2044434" "GSM2044435" "GSM2044436" "GSM2044446" ...
## ..$ ReleaseDate : chr [1:5] "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" ...
## ..$ LoadDate : chr [1:5] "2016-01-21 18:56:26" "2016-01-21 18:55:15" "2016-01-21 18:54:36" "2016-01-21 18:54:44" ...
## ..$ spots : int [1:5] 29127539 25319531 23007303 22872590 22935464
## ..$ bases : num [1:5] 2.91e+09 2.53e+09 2.30e+09 2.29e+09 2.29e+09
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 100 100 100 100 100
## ..$ size_MB : int [1:5] 1207 1048 976 951 970
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112222/SRR3112222.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112223/SRR3112223.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112224/SRR3112224.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112234/SRR3112234.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ BioProject : chr [1:5] "PRJNA309443" "PRJNA309443" "PRJNA309443" "PRJNA309443" ...
## ..$ Study_Pubmed_id : int [1:5] 2 2 2 2 2
## ..$ ProjectID : int [1:5] 309443 309443 309443 309443 309443
## ..$ Sample : chr [1:5] "SRS1256809" "SRS1256808" "SRS1256807" "SRS1256797" ...
## ..$ BioSample : chr [1:5] "SAMN04433002" "SAMN04433003" "SAMN04433004" "SAMN04432984" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA337501" "SRA337501" "SRA337501" "SRA337501" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "F30DCB326FF5E049FCE351CBD262C40E" "A329F0AA3F3FBF4DF1A6F6CBE1F86A61" "F3DD148FA2EF06D1ECD973ED930D660C" "7614D6801985EC1780FB5F0E99A56C26" ...
## ..$ ReadHash : chr [1:5] "88EA0F43E25F8BA3B3D92F85F59BF097" "B4EF544E9879FECCA82D276CE6032DC0" "120CACB855B17F9618686C6AD220EE62" "B5AD61A26F5D84AE2999AA74A38254F2" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP068733:Genes expressed differentially in diabetic endothelial cells treated with ep300 siRNA compared to non-target siRNA:Non-target;SRX1540363,SRX1540364,SRX1540365:ep300siRNA;SRX1540366,SRX1540367,SRX1540368## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR3112231: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR3112232: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR3112233: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR3112234: int [1:58302] 0 1 6 0 0 0 0 0 0 0 ...
## ..$ SRR3112236: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR3112231: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112232: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112233: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112234: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112236: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR3112231: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112232: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112233: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112234: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112236: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:5] "SRX1540363" "SRX1540364" "SRX1540365" "SRX1540366" ...
## ..$ SRS_accession: chr [1:5] "SRS1256799" "SRS1256800" "SRS1256796" "SRS1256797" ...
## ..$ SRP_accession: chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:5] "GSM2044443" "GSM2044444" "GSM2044445" "GSM2044446" ...
## ..$ GEO_series : chr [1:5] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:5] "SRX1540363" "SRX1540364" "SRX1540365" "SRX1540366" ...
## ..$ SRS_accession : chr [1:5] "SRS1256799" "SRS1256800" "SRS1256796" "SRS1256797" ...
## ..$ SRP_accession : chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:5] "GSM2044443" "GSM2044444" "GSM2044445" "GSM2044446" ...
## ..$ GEO_series : chr [1:5] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM2044443" "GSM2044444" "GSM2044445" "GSM2044446" ...
## ..$ ReleaseDate : chr [1:5] "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" ...
## ..$ LoadDate : chr [1:5] "2016-01-21 18:56:07" "2016-01-21 18:59:05" "2016-01-21 18:54:20" "2016-01-21 18:54:44" ...
## ..$ spots : int [1:5] 26279280 22357317 21892915 22872590 22935464
## ..$ bases : num [1:5] 2.63e+09 2.24e+09 2.19e+09 2.29e+09 2.29e+09
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 100 100 100 100 100
## ..$ size_MB : int [1:5] 1085 925 927 951 970
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112231/SRR3112231.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112232/SRR3112232.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112233/SRR3112233.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112234/SRR3112234.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ BioProject : chr [1:5] "PRJNA309443" "PRJNA309443" "PRJNA309443" "PRJNA309443" ...
## ..$ Study_Pubmed_id : int [1:5] 2 2 2 2 2
## ..$ ProjectID : int [1:5] 309443 309443 309443 309443 309443
## ..$ Sample : chr [1:5] "SRS1256799" "SRS1256800" "SRS1256796" "SRS1256797" ...
## ..$ BioSample : chr [1:5] "SAMN04433011" "SAMN04433012" "SAMN04433013" "SAMN04432984" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA337501" "SRA337501" "SRA337501" "SRA337501" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "41246C7523C66CAA8B67015E0BEF4E7B" "A3C41CC001732851E5A227CB0E069A54" "C5E6D3CE91EB3098E905D478C8087708" "7614D6801985EC1780FB5F0E99A56C26" ...
## ..$ ReadHash : chr [1:5] "63E68DE4E2069C1E5BAD6E755C704D88" "2A94DE3239C7E390EB44C1FE08231026" "D98234ED6013408CD2B89D6A051EDBD3" "B5AD61A26F5D84AE2999AA74A38254F2" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP068733:Genes expressed differentially in healthy endothelial cells treated with SAHA:Ctrl; SRX1540339,SRX1540340,SRX1540341:SAHA; SRX1540342,SRX1540343,SRX1540344## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR3112207: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR3112208: int [1:58302] 0 2 4 0 0 0 0 0 0 0 ...
## ..$ SRR3112209: int [1:58302] 0 0 4 0 0 0 0 0 0 0 ...
## ..$ SRR3112210: int [1:58302] 0 1 3 0 0 0 0 0 0 0 ...
## ..$ SRR3112211: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR3112212: int [1:58302] 0 3 3 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR3112207: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112208: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112209: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112210: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112211: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112212: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR3112207: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112208: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112209: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112210: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112211: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112212: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX1540339" "SRX1540340" "SRX1540341" "SRX1540342" ...
## ..$ SRS_accession: chr [1:6] "SRS1256824" "SRS1256823" "SRS1256822" "SRS1256821" ...
## ..$ SRP_accession: chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:6] "GSM2044419" "GSM2044420" "GSM2044421" "GSM2044422" ...
## ..$ GEO_series : chr [1:6] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX1540339" "SRX1540340" "SRX1540341" "SRX1540342" ...
## ..$ SRS_accession : chr [1:6] "SRS1256824" "SRS1256823" "SRS1256822" "SRS1256821" ...
## ..$ SRP_accession : chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:6] "GSM2044419" "GSM2044420" "GSM2044421" "GSM2044422" ...
## ..$ GEO_series : chr [1:6] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2044419" "GSM2044420" "GSM2044421" "GSM2044422" ...
## ..$ ReleaseDate : chr [1:6] "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" ...
## ..$ LoadDate : chr [1:6] "2016-01-21 19:02:55" "2016-01-21 18:56:48" "2016-01-21 19:02:52" "2016-01-21 18:56:23" ...
## ..$ spots : int [1:6] 27002876 29787850 31924383 30522043 27496291 24414522
## ..$ bases : num [1:6] 2.70e+09 2.98e+09 3.19e+09 3.05e+09 2.75e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 100 100 100 100 100 100
## ..$ size_MB : int [1:6] 1149 1308 1406 1297 1214 1071
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112207/SRR3112207.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112208/SRR3112208.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112209/SRR3112209.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112210/SRR3112210.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ BioProject : chr [1:6] "PRJNA309443" "PRJNA309443" "PRJNA309443" "PRJNA309443" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 309443 309443 309443 309443 309443 309443
## ..$ Sample : chr [1:6] "SRS1256824" "SRS1256823" "SRS1256822" "SRS1256821" ...
## ..$ BioSample : chr [1:6] "SAMN04432987" "SAMN04432988" "SAMN04432989" "SAMN04432990" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA337501" "SRA337501" "SRA337501" "SRA337501" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "156E06B86ACD1D98EA022258E14F2969" "B51577A89740DCA75495A4C159323D95" "7CBD34EEFF8BCC40C60F5D4255106439" "3F2D33F4390B5B0AABE745046A08C971" ...
## ..$ ReadHash : chr [1:6] "8C6E5A66FD825886D6E16460FB175F0D" "E2905B814618737D62C4E91FC5B53F6D" "F9239185D4F5E29818FD53DA4344F643" "AE07DDCC457E0738EC9B5555DA8CD30C" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP068733:Genes expressed differentially in healthy endothelial cells treated with C646:Ctrl; SRX1540339,SRX1540340,SRX1540341:C646; SRX1540345,SRX1540346,SRX1540347## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR3112207: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR3112208: int [1:58302] 0 2 4 0 0 0 0 0 0 0 ...
## ..$ SRR3112209: int [1:58302] 0 0 4 0 0 0 0 0 0 0 ...
## ..$ SRR3112213: int [1:58302] 0 3 3 0 0 0 0 0 0 0 ...
## ..$ SRR3112214: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR3112207: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112208: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112209: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112213: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112214: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR3112207: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112208: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112209: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112213: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112214: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "PASS" "PASS" "PASS" "WARN(8)" ...
## ..$ SRX_accession: chr [1:5] "SRX1540339" "SRX1540340" "SRX1540341" "SRX1540345" ...
## ..$ SRS_accession: chr [1:5] "SRS1256824" "SRS1256823" "SRS1256822" "SRS1256817" ...
## ..$ SRP_accession: chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:5] "GSM2044419" "GSM2044420" "GSM2044421" "GSM2044425" ...
## ..$ GEO_series : chr [1:5] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "PASS" "PASS" "PASS" "WARN(8)" ...
## ..$ SRX_accession : chr [1:5] "SRX1540339" "SRX1540340" "SRX1540341" "SRX1540345" ...
## ..$ SRS_accession : chr [1:5] "SRS1256824" "SRS1256823" "SRS1256822" "SRS1256817" ...
## ..$ SRP_accession : chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:5] "GSM2044419" "GSM2044420" "GSM2044421" "GSM2044425" ...
## ..$ GEO_series : chr [1:5] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM2044419" "GSM2044420" "GSM2044421" "GSM2044425" ...
## ..$ ReleaseDate : chr [1:5] "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" ...
## ..$ LoadDate : chr [1:5] "2016-01-21 19:02:55" "2016-01-21 18:56:48" "2016-01-21 19:02:52" "2016-01-21 18:55:48" ...
## ..$ spots : int [1:5] 27002876 29787850 31924383 30224406 28433349
## ..$ bases : num [1:5] 2.70e+09 2.98e+09 3.19e+09 3.02e+09 2.84e+09
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 100 100 100 100 100
## ..$ size_MB : int [1:5] 1149 1308 1406 1289 1249
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112207/SRR3112207.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112208/SRR3112208.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112209/SRR3112209.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112213/SRR3112213.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:5] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ BioProject : chr [1:5] "PRJNA309443" "PRJNA309443" "PRJNA309443" "PRJNA309443" ...
## ..$ Study_Pubmed_id : int [1:5] 2 2 2 2 2
## ..$ ProjectID : int [1:5] 309443 309443 309443 309443 309443
## ..$ Sample : chr [1:5] "SRS1256824" "SRS1256823" "SRS1256822" "SRS1256817" ...
## ..$ BioSample : chr [1:5] "SAMN04432987" "SAMN04432988" "SAMN04432989" "SAMN04432993" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA337501" "SRA337501" "SRA337501" "SRA337501" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "156E06B86ACD1D98EA022258E14F2969" "B51577A89740DCA75495A4C159323D95" "7CBD34EEFF8BCC40C60F5D4255106439" "4DCDF9A31D23453153663B406F642D27" ...
## ..$ ReadHash : chr [1:5] "8C6E5A66FD825886D6E16460FB175F0D" "E2905B814618737D62C4E91FC5B53F6D" "F9239185D4F5E29818FD53DA4344F643" "28903CAF8C37EFEB03537EE9FC8BBEBF" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP068733:Genes expressed differentially in healthy endothelial cells treated with ep300 siRNA compared to healthy cells treated with DMSO:Ctrl;SRX1540339,SRX1540340,SRX1540341:ep300siRNA; SRX1540351,SRX1540352,SRX1540353## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR3112207: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR3112208: int [1:58302] 0 2 4 0 0 0 0 0 0 0 ...
## ..$ SRR3112209: int [1:58302] 0 0 4 0 0 0 0 0 0 0 ...
## ..$ SRR3112219: int [1:58302] 0 0 4 0 0 0 0 0 0 0 ...
## ..$ SRR3112220: int [1:58302] 0 1 3 0 0 0 0 0 0 1 ...
## ..$ SRR3112221: int [1:58302] 0 1 4 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR3112207: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112208: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112209: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112219: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112220: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112221: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR3112207: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112208: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112209: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112219: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112220: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112221: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX1540339" "SRX1540340" "SRX1540341" "SRX1540351" ...
## ..$ SRS_accession: chr [1:6] "SRS1256824" "SRS1256823" "SRS1256822" "SRS1256813" ...
## ..$ SRP_accession: chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:6] "GSM2044419" "GSM2044420" "GSM2044421" "GSM2044431" ...
## ..$ GEO_series : chr [1:6] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX1540339" "SRX1540340" "SRX1540341" "SRX1540351" ...
## ..$ SRS_accession : chr [1:6] "SRS1256824" "SRS1256823" "SRS1256822" "SRS1256813" ...
## ..$ SRP_accession : chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:6] "GSM2044419" "GSM2044420" "GSM2044421" "GSM2044431" ...
## ..$ GEO_series : chr [1:6] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2044419" "GSM2044420" "GSM2044421" "GSM2044431" ...
## ..$ ReleaseDate : chr [1:6] "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" ...
## ..$ LoadDate : chr [1:6] "2016-01-21 19:02:55" "2016-01-21 18:56:48" "2016-01-21 19:02:52" "2016-01-21 18:55:52" ...
## ..$ spots : int [1:6] 27002876 29787850 31924383 31142583 30746331 22059235
## ..$ bases : num [1:6] 2.70e+09 2.98e+09 3.19e+09 3.11e+09 3.07e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 100 100 100 100 100 100
## ..$ size_MB : int [1:6] 1149 1308 1406 1316 1344 966
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112207/SRR3112207.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112208/SRR3112208.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112209/SRR3112209.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112219/SRR3112219.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ BioProject : chr [1:6] "PRJNA309443" "PRJNA309443" "PRJNA309443" "PRJNA309443" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 309443 309443 309443 309443 309443 309443
## ..$ Sample : chr [1:6] "SRS1256824" "SRS1256823" "SRS1256822" "SRS1256813" ...
## ..$ BioSample : chr [1:6] "SAMN04432987" "SAMN04432988" "SAMN04432989" "SAMN04432999" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA337501" "SRA337501" "SRA337501" "SRA337501" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "156E06B86ACD1D98EA022258E14F2969" "B51577A89740DCA75495A4C159323D95" "7CBD34EEFF8BCC40C60F5D4255106439" "05C37A2E6D29C69CF6560A7566EEA4D7" ...
## ..$ ReadHash : chr [1:6] "8C6E5A66FD825886D6E16460FB175F0D" "E2905B814618737D62C4E91FC5B53F6D" "F9239185D4F5E29818FD53DA4344F643" "1BBC7EB57A6ABAE88900FCD9958E5EC1" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP068733:Genes expressed differentially in diabetic endothelial cells treated with ep300 siRNA compared to non-target siRNA:Non-target;SRX1540348,SRX1540349,SRX1540350:ep300siRNA; SRX1540351,SRX1540352,SRX1540353## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR3112216: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR3112217: int [1:58302] 0 1 4 0 0 0 0 0 0 0 ...
## ..$ SRR3112218: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112219: int [1:58302] 0 0 4 0 0 0 0 0 0 0 ...
## ..$ SRR3112220: int [1:58302] 0 1 3 0 0 0 0 0 0 1 ...
## ..$ SRR3112221: int [1:58302] 0 1 4 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR3112216: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112217: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112218: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112219: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112220: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3112221: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR3112216: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112217: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112218: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112219: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112220: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR3112221: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX1540348" "SRX1540349" "SRX1540350" "SRX1540351" ...
## ..$ SRS_accession: chr [1:6] "SRS1256815" "SRS1256814" "SRS1256812" "SRS1256813" ...
## ..$ SRP_accession: chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:6] "GSM2044428" "GSM2044429" "GSM2044430" "GSM2044431" ...
## ..$ GEO_series : chr [1:6] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX1540348" "SRX1540349" "SRX1540350" "SRX1540351" ...
## ..$ SRS_accession : chr [1:6] "SRS1256815" "SRS1256814" "SRS1256812" "SRS1256813" ...
## ..$ SRP_accession : chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ Sample_name : chr [1:6] "GSM2044428" "GSM2044429" "GSM2044430" "GSM2044431" ...
## ..$ GEO_series : chr [1:6] "GSE77108" "GSE77108" "GSE77108" "GSE77108" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2044428" "GSM2044429" "GSM2044430" "GSM2044431" ...
## ..$ ReleaseDate : chr [1:6] "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" "2017-12-15 13:02:09" ...
## ..$ LoadDate : chr [1:6] "2016-01-21 18:58:23" "2016-01-21 18:56:34" "2016-01-21 18:55:06" "2016-01-21 18:55:52" ...
## ..$ spots : int [1:6] 31352322 27830227 26430351 31142583 30746331 22059235
## ..$ bases : num [1:6] 3.14e+09 2.78e+09 2.64e+09 3.11e+09 3.07e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 100 100 100 100 100 100
## ..$ size_MB : int [1:6] 1324 1214 1164 1316 1344 966
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112216/SRR3112216.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3112217/SRR3112217.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112218/SRR3112218.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3112219/SRR3112219.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP068733" "SRP068733" "SRP068733" "SRP068733" ...
## ..$ BioProject : chr [1:6] "PRJNA309443" "PRJNA309443" "PRJNA309443" "PRJNA309443" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 309443 309443 309443 309443 309443 309443
## ..$ Sample : chr [1:6] "SRS1256815" "SRS1256814" "SRS1256812" "SRS1256813" ...
## ..$ BioSample : chr [1:6] "SAMN04432996" "SAMN04432997" "SAMN04432998" "SAMN04432999" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA337501" "SRA337501" "SRA337501" "SRA337501" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "37240079DDC5C47944EFAB0B473BF011" "47B2D55304C938838FB740923F967B3C" "C2B6D3033F8C350B52748DCDAA54B958" "05C37A2E6D29C69CF6560A7566EEA4D7" ...
## ..$ ReadHash : chr [1:6] "CE9203FBEE38863926D42D30136B7E77" "945DC5BFE0F475B3AF4FCF194E918049" "676BE2FD7EF3BB35F51B73DA4D42B538" "1BBC7EB57A6ABAE88900FCD9958E5EC1" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP069228:Genes expressed differentially in healthy human endothelial cells treated with metaformin:Ctrl; SRX1558510,SRX1558511,SRX1558512:Meta; SRX1558513,SRX1558514,SRX1558515## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR3141635: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141636: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141637: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141638: int [1:58302] 0 0 0 0 0 0 0 0 1 0 ...
## ..$ SRR3141639: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141640: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR3141635: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141636: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141637: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141638: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141639: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141640: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR3141635: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR3141636: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR3141637: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR3141638: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR3141639: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR3141640: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "WARN(8)" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX1558510" "SRX1558511" "SRX1558512" "SRX1558513" ...
## ..$ SRS_accession: chr [1:6] "SRS1273714" "SRS1273713" "SRS1273712" "SRS1273711" ...
## ..$ SRP_accession: chr [1:6] "SRP069228" "SRP069228" "SRP069228" "SRP069228" ...
## ..$ Sample_name : chr [1:6] "GSM2053612" "GSM2053613" "GSM2053614" "GSM2053615" ...
## ..$ GEO_series : chr [1:6] "GSE77522" "GSE77522" "GSE77522" "GSE77522" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "WARN(8)" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX1558510" "SRX1558511" "SRX1558512" "SRX1558513" ...
## ..$ SRS_accession : chr [1:6] "SRS1273714" "SRS1273713" "SRS1273712" "SRS1273711" ...
## ..$ SRP_accession : chr [1:6] "SRP069228" "SRP069228" "SRP069228" "SRP069228" ...
## ..$ Sample_name : chr [1:6] "GSM2053612" "GSM2053613" "GSM2053614" "GSM2053615" ...
## ..$ GEO_series : chr [1:6] "GSE77522" "GSE77522" "GSE77522" "GSE77522" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2053612" "GSM2053613" "GSM2053614" "GSM2053615" ...
## ..$ ReleaseDate : chr [1:6] "2019-02-04 09:52:06" "2019-02-04 09:52:06" "2019-02-04 09:52:06" "2019-02-04 09:52:06" ...
## ..$ LoadDate : chr [1:6] "2016-02-03 11:20:16" "2016-02-03 11:19:19" "2016-02-03 11:22:16" "2016-02-03 11:19:18" ...
## ..$ spots : int [1:6] 27180379 28711709 33459082 25503301 29571491 29512915
## ..$ bases : int [1:6] 978493644 1033621524 1204526952 918118836 1064573676 1062464940
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 36 36 36 36 36 36
## ..$ size_MB : int [1:6] 643 682 789 601 706 703
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3141635/SRR3141635.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3141636/SRR3141636.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3141637/SRR3141637.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3141638/SRR3141638.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" ...
## ..$ SRAStudy : chr [1:6] "SRP069228" "SRP069228" "SRP069228" "SRP069228" ...
## ..$ BioProject : chr [1:6] "PRJNA310702" "PRJNA310702" "PRJNA310702" "PRJNA310702" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 310702 310702 310702 310702 310702 310702
## ..$ Sample : chr [1:6] "SRS1273714" "SRS1273713" "SRS1273712" "SRS1273711" ...
## ..$ BioSample : chr [1:6] "SAMN04454409" "SAMN04454410" "SAMN04454411" "SAMN04454412" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA346262" "SRA346262" "SRA346262" "SRA346262" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "822C9FE4F323D74F53F761D469CE7B1D" "70058236EAD2B93ABE5C12C21E96610D" "3A6AFC78A0526E95D9DC17719F2B23B0" "94A9ED03289E466B7460DBD46D1AC8A2" ...
## ..$ ReadHash : chr [1:6] "6E91B0FC11B1F6633AF29D293AF6DDFD" "5E5B3BF6EEA1FAB9B1C0B443FDE85E95" "BD4CB359FA81AB080150E3BF30E9BD03" "8BE5D2D48D7F1E345BD2DBEA8F9E3F5C" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP069228:Genes expressed differentially in healthy human endothelial cells treated with metaformin and 30mM of D-glucose:Ctrl; SRX1558516,SRX1558517,SRX1558518:Meta;SRX1558519,SRX1558520,SRX1558521## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR3141641: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141642: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141643: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141644: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141645: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141646: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR3141641: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141642: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141643: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141644: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141645: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3141646: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR3141641: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR3141642: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR3141643: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR3141644: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR3141645: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR3141646: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "WARN(8)" "WARN(3,4)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:6] "SRX1558516" "SRX1558517" "SRX1558518" "SRX1558519" ...
## ..$ SRS_accession: chr [1:6] "SRS1273708" "SRS1273707" "SRS1273706" "SRS1273705" ...
## ..$ SRP_accession: chr [1:6] "SRP069228" "SRP069228" "SRP069228" "SRP069228" ...
## ..$ Sample_name : chr [1:6] "GSM2053618" "GSM2053619" "GSM2053620" "GSM2053621" ...
## ..$ GEO_series : chr [1:6] "GSE77522" "GSE77522" "GSE77522" "GSE77522" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "WARN(8)" "WARN(3,4)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:6] "SRX1558516" "SRX1558517" "SRX1558518" "SRX1558519" ...
## ..$ SRS_accession : chr [1:6] "SRS1273708" "SRS1273707" "SRS1273706" "SRS1273705" ...
## ..$ SRP_accession : chr [1:6] "SRP069228" "SRP069228" "SRP069228" "SRP069228" ...
## ..$ Sample_name : chr [1:6] "GSM2053618" "GSM2053619" "GSM2053620" "GSM2053621" ...
## ..$ GEO_series : chr [1:6] "GSE77522" "GSE77522" "GSE77522" "GSE77522" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2053618" "GSM2053619" "GSM2053620" "GSM2053621" ...
## ..$ ReleaseDate : chr [1:6] "2019-02-04 09:52:06" "2019-02-04 09:52:06" "2019-02-04 09:52:06" "2019-02-04 09:52:06" ...
## ..$ LoadDate : chr [1:6] "2016-02-03 11:19:32" "2016-02-03 11:19:43" "2016-02-03 11:18:13" "2016-02-03 11:18:13" ...
## ..$ spots : int [1:6] 28689386 30885046 24083534 24833684 31515399 29883830
## ..$ bases : int [1:6] 1032817896 1111861656 867007224 894012624 1134554364 1075817880
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 36 36 36 36 36 36
## ..$ size_MB : int [1:6] 680 732 571 591 745 711
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3141641/SRR3141641.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3141642/SRR3141642.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3141643/SRR3141643.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3141644/SRR3141644.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" ...
## ..$ SRAStudy : chr [1:6] "SRP069228" "SRP069228" "SRP069228" "SRP069228" ...
## ..$ BioProject : chr [1:6] "PRJNA310702" "PRJNA310702" "PRJNA310702" "PRJNA310702" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 310702 310702 310702 310702 310702 310702
## ..$ Sample : chr [1:6] "SRS1273708" "SRS1273707" "SRS1273706" "SRS1273705" ...
## ..$ BioSample : chr [1:6] "SAMN04454415" "SAMN04454416" "SAMN04454417" "SAMN04454418" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA346262" "SRA346262" "SRA346262" "SRA346262" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "98AB8D25653E0CE6C32DB6FD59043065" "B0E85258037743E2352FFA81D4A32F97" "3A62C388252BDB2F245F177BA560CE2B" "B92B36631E7001314F85917656FF98F8" ...
## ..$ ReadHash : chr [1:6] "6AD9262A16F635CAF1C4036984A8710C" "60388CF3553C473DED03D283EFECD4E7" "9CC5BBC762A0585E442B06A5A276D75E" "976179E14E473BFC6C81D6B8849A4C19" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP079700:Gene expression differentially regulated in human pluripotent stem-cell-derived cardiomyocytes by glucose concentration 0 mM for 5 days and back to Glucose 25 mM for 5 days:Ctrl;SRX1975929,SRX1975930,SRX1975931:G0mMto25mM; SRX1975932,SRX1975933,SRX1975934## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR3950943: int [1:58302] 0 113 3 0 0 0 0 0 0 7 ...
## ..$ SRR3950944: int [1:58302] 1 86 7 1 0 0 0 0 0 6 ...
## ..$ SRR3950945: int [1:58302] 0 90 2 1 0 0 0 0 0 8 ...
## ..$ SRR3950946: int [1:58302] 0 67 3 0 0 0 0 0 0 4 ...
## ..$ SRR3950947: int [1:58302] 0 99 4 3 0 0 0 0 0 8 ...
## ..$ SRR3950948: int [1:58302] 0 111 6 0 0 0 0 0 0 5 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR3950943: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3950944: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3950945: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3950946: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3950947: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3950948: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR3950943: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR3950944: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR3950945: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR3950946: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR3950947: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR3950948: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX1975929" "SRX1975930" "SRX1975931" "SRX1975932" ...
## ..$ SRS_accession: chr [1:6] "SRS1584018" "SRS1584019" "SRS1584020" "SRS1584021" ...
## ..$ SRP_accession: chr [1:6] "SRP079700" "SRP079700" "SRP079700" "SRP079700" ...
## ..$ Sample_name : chr [1:6] "GSM2251702" "GSM2251703" "GSM2251704" "GSM2251705" ...
## ..$ GEO_series : chr [1:6] "GSE84814" "GSE84814" "GSE84814" "GSE84814" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX1975929" "SRX1975930" "SRX1975931" "SRX1975932" ...
## ..$ SRS_accession : chr [1:6] "SRS1584018" "SRS1584019" "SRS1584020" "SRS1584021" ...
## ..$ SRP_accession : chr [1:6] "SRP079700" "SRP079700" "SRP079700" "SRP079700" ...
## ..$ Sample_name : chr [1:6] "GSM2251702" "GSM2251703" "GSM2251704" "GSM2251705" ...
## ..$ GEO_series : chr [1:6] "GSE84814" "GSE84814" "GSE84814" "GSE84814" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2251702" "GSM2251703" "GSM2251704" "GSM2251705" ...
## ..$ ReleaseDate : chr [1:6] "2017-01-03 09:57:23" "2017-01-03 09:57:23" "2017-01-03 09:57:23" "2017-01-03 09:57:23" ...
## ..$ LoadDate : chr [1:6] "2016-07-25 17:01:41" "2016-07-25 16:59:17" "2016-07-25 16:57:10" "2016-07-25 16:56:12" ...
## ..$ spots : int [1:6] 28431336 26607975 24499818 23267469 29311360 31487399
## ..$ bases : num [1:6] 8.19e+09 7.59e+09 7.07e+09 6.69e+09 8.45e+09 ...
## ..$ spots_with_mates : int [1:6] 28431336 26607975 24499818 23267469 29311360 31487399
## ..$ avgLength : int [1:6] 287 285 288 287 288 288
## ..$ size_MB : int [1:6] 3197 2952 2749 2617 3298 3535
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3950943/SRR3950943.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3950944/SRR3950944.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3950945/SRR3950945.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3950946/SRR3950946.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 3000" "Illumina HiSeq 3000" "Illumina HiSeq 3000" "Illumina HiSeq 3000" ...
## ..$ SRAStudy : chr [1:6] "SRP079700" "SRP079700" "SRP079700" "SRP079700" ...
## ..$ BioProject : chr [1:6] "PRJNA331184" "PRJNA331184" "PRJNA331184" "PRJNA331184" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 331184 331184 331184 331184 331184 331184
## ..$ Sample : chr [1:6] "SRS1584018" "SRS1584019" "SRS1584020" "SRS1584021" ...
## ..$ BioSample : chr [1:6] "SAMN05439268" "SAMN05439267" "SAMN05439263" "SAMN05439262" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA443958" "SRA443958" "SRA443958" "SRA443958" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "7A4890726F6F83BD5AA83C60F934F824" "FDF5727F693AC4865A0F3602EDAF81F9" "C94DC9BC25EB18FF0ED9AECA0FA7CE1D" "E228C3790A2B4A05BF1EE13571356109" ...
## ..$ ReadHash : chr [1:6] "5634FDB5B305A4ACE48C1AE4BE619180" "A9BD597C86959B157945F4AFD1F37D38" "DE749CBB56A3BC909D45B5AC0B1DE73E" "37B7C2B4A6C08145E78F2DC717A4AE9D" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP079700:Gene expression differentially regulated in human pluripotent stem-cell-derived cardiomyocytes by glucose concetration of 25 mM:Ctrl;SRX1975929,SRX1975930,SRX1975931:G25mM;SRX1975935,SRX1975936,SRX1975937## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR3950943: int [1:58302] 0 113 3 0 0 0 0 0 0 7 ...
## ..$ SRR3950944: int [1:58302] 1 86 7 1 0 0 0 0 0 6 ...
## ..$ SRR3950945: int [1:58302] 0 90 2 1 0 0 0 0 0 8 ...
## ..$ SRR3950949: int [1:58302] 0 264 10 2 0 0 0 0 0 11 ...
## ..$ SRR3950950: int [1:58302] 0 253 5 1 0 0 0 0 0 12 ...
## ..$ SRR3950951: int [1:58302] 0 85 2 0 0 0 0 0 0 5 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR3950943: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3950944: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3950945: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3950949: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3950950: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3950951: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR3950943: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR3950944: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR3950945: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR3950949: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR3950950: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "150" ...
## ..$ SRR3950951: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "150" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX1975929" "SRX1975930" "SRX1975931" "SRX1975935" ...
## ..$ SRS_accession: chr [1:6] "SRS1584018" "SRS1584019" "SRS1584020" "SRS1584024" ...
## ..$ SRP_accession: chr [1:6] "SRP079700" "SRP079700" "SRP079700" "SRP079700" ...
## ..$ Sample_name : chr [1:6] "GSM2251702" "GSM2251703" "GSM2251704" "GSM2251708" ...
## ..$ GEO_series : chr [1:6] "GSE84814" "GSE84814" "GSE84814" "GSE84814" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX1975929" "SRX1975930" "SRX1975931" "SRX1975935" ...
## ..$ SRS_accession : chr [1:6] "SRS1584018" "SRS1584019" "SRS1584020" "SRS1584024" ...
## ..$ SRP_accession : chr [1:6] "SRP079700" "SRP079700" "SRP079700" "SRP079700" ...
## ..$ Sample_name : chr [1:6] "GSM2251702" "GSM2251703" "GSM2251704" "GSM2251708" ...
## ..$ GEO_series : chr [1:6] "GSE84814" "GSE84814" "GSE84814" "GSE84814" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2251702" "GSM2251703" "GSM2251704" "GSM2251708" ...
## ..$ ReleaseDate : chr [1:6] "2017-01-03 09:57:23" "2017-01-03 09:57:23" "2017-01-03 09:57:23" "2017-01-03 09:57:23" ...
## ..$ LoadDate : chr [1:6] "2016-07-25 17:01:41" "2016-07-25 16:59:17" "2016-07-25 16:57:10" "2016-07-25 17:30:54" ...
## ..$ spots : int [1:6] 28431336 26607975 24499818 72753751 70386487 23939852
## ..$ bases : num [1:6] 8.19e+09 7.59e+09 7.07e+09 2.09e+10 2.03e+10 ...
## ..$ spots_with_mates : int [1:6] 28431336 26607975 24499818 72753751 70386487 23939852
## ..$ avgLength : int [1:6] 287 285 288 287 288 287
## ..$ size_MB : int [1:6] 3197 2952 2749 8193 7927 2686
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3950943/SRR3950943.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3950944/SRR3950944.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3950945/SRR3950945.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3950949/SRR3950949.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 3000" "Illumina HiSeq 3000" "Illumina HiSeq 3000" "Illumina HiSeq 3000" ...
## ..$ SRAStudy : chr [1:6] "SRP079700" "SRP079700" "SRP079700" "SRP079700" ...
## ..$ BioProject : chr [1:6] "PRJNA331184" "PRJNA331184" "PRJNA331184" "PRJNA331184" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 331184 331184 331184 331184 331184 331184
## ..$ Sample : chr [1:6] "SRS1584018" "SRS1584019" "SRS1584020" "SRS1584024" ...
## ..$ BioSample : chr [1:6] "SAMN05439268" "SAMN05439267" "SAMN05439263" "SAMN05439277" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA443958" "SRA443958" "SRA443958" "SRA443958" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "7A4890726F6F83BD5AA83C60F934F824" "FDF5727F693AC4865A0F3602EDAF81F9" "C94DC9BC25EB18FF0ED9AECA0FA7CE1D" "E811CEF56CCCFC3C86EA6DDB3FBBAE4E" ...
## ..$ ReadHash : chr [1:6] "5634FDB5B305A4ACE48C1AE4BE619180" "A9BD597C86959B157945F4AFD1F37D38" "DE749CBB56A3BC909D45B5AC0B1DE73E" "EFBE9D2B5D559017871AABADB1417EF2" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP010483:Gene expression differentially regulated in human islet of Langerhans by pro-inflammatory cytokines interleukin-1β:Ctrl; SRX117470,SRX117472,SRX117474,SRX117476,SRX117478:interleukin-1β;SRX117471,SRX117473,SRX117475,SRX117477,SRX117479## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR401815: int [1:58302] 0 2 2 0 0 0 0 0 0 1 ...
## ..$ SRR401816: int [1:58302] 0 0 6 0 0 0 0 0 0 0 ...
## ..$ SRR401817: int [1:58302] 0 6 16 0 0 0 0 0 0 0 ...
## ..$ SRR401818: int [1:58302] 1 7 12 1 0 0 0 0 0 0 ...
## ..$ SRR401819: int [1:58302] 0 8 32 0 0 0 0 0 0 0 ...
## ..$ SRR401820: int [1:58302] 0 16 14 0 0 0 0 0 0 1 ...
## ..$ SRR401821: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR401822: int [1:58302] 0 0 5 0 0 0 0 0 0 0 ...
## ..$ SRR401823: int [1:58302] 0 12 22 0 0 0 0 0 0 1 ...
## ..$ SRR401824: int [1:58302] 0 2 5 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR401815: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR401816: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR401817: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR401818: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR401819: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR401820: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR401821: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR401822: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR401823: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR401824: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR401815: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR401816: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR401817: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR401818: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR401819: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR401820: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR401821: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR401822: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR401823: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR401824: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "WARN(1,5,7)" "WARN(1,5,7)" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX117470" "SRX117471" "SRX117472" "SRX117473" ...
## ..$ SRS_accession: chr [1:10] "SRS290090" "SRS290091" "SRS290092" "SRS290093" ...
## ..$ SRP_accession: chr [1:10] "SRP010483" "SRP010483" "SRP010483" "SRP010483" ...
## ..$ Sample_name : chr [1:10] "GSM865291" "GSM865292" "GSM865293" "GSM865294" ...
## ..$ GEO_series : chr [1:10] "GSE35296" "GSE35296" "GSE35296" "GSE35296" ...
## ..$ Library_name : chr [1:10] "GSM865291: islet preparation 1 under control condition" "GSM865292: islet preparation 1 under cytokine treatment" "GSM865293: islet preparation 2 under control condition" "GSM865294: islet preparation 2 under cytokine treatment" ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "WARN(1,5,7)" "WARN(1,5,7)" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX117470" "SRX117471" "SRX117472" "SRX117473" ...
## ..$ SRS_accession : chr [1:10] "SRS290090" "SRS290091" "SRS290092" "SRS290093" ...
## ..$ SRP_accession : chr [1:10] "SRP010483" "SRP010483" "SRP010483" "SRP010483" ...
## ..$ Sample_name : chr [1:10] "GSM865291" "GSM865292" "GSM865293" "GSM865294" ...
## ..$ GEO_series : chr [1:10] "GSE35296" "GSE35296" "GSE35296" "GSE35296" ...
## ..$ Library_name : chr [1:10] "GSM865291: islet preparation 1 under control condition" "GSM865292: islet preparation 1 under cytokine treatment" "GSM865293: islet preparation 2 under control condition" "GSM865294: islet preparation 2 under cytokine treatment" ...
## ..$ SampleName : chr [1:10] "GSM865291" "GSM865292" "GSM865293" "GSM865294" ...
## ..$ ReleaseDate : chr [1:10] "2012-03-09 09:39:54" "2012-03-09 09:39:54" "2012-03-09 09:39:54" "2012-03-09 09:39:54" ...
## ..$ LoadDate : chr [1:10] "2012-08-11 17:17:40" "2012-08-11 17:17:39" "2012-08-11 17:18:08" "2012-08-11 17:18:07" ...
## ..$ spots : int [1:10] 6785237 5958263 29665483 27709013 28702757 30859535 11538404 17676871 25717722 9601613
## ..$ bases : num [1:10] 6.92e+08 6.08e+08 3.03e+09 2.83e+09 2.93e+09 ...
## ..$ spots_with_mates : int [1:10] 6785237 5958263 29665483 27709013 28702757 30859535 11538404 17676871 25717722 9601613
## ..$ avgLength : int [1:10] 102 102 102 102 102 102 102 102 102 102
## ..$ size_MB : int [1:10] 452 395 1228 1138 1165 1217 770 1225 1194 679
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR401815/SRR401815.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR401816/SRR401816.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR401817/SRR401817.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR401818/SRR401818.2" ...
## ..$ LibraryName : chr [1:10] "GSM865291: islet preparation 1 under control condition" "GSM865292: islet preparation 1 under cytokine treatment" "GSM865293: islet preparation 2 under control condition" "GSM865294: islet preparation 2 under cytokine treatment" ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:10] 81 74 116 107 100 136 92 88 98 87
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina Genome Analyzer II" "Illumina Genome Analyzer II" "Illumina Genome Analyzer II" "Illumina Genome Analyzer II" ...
## ..$ SRAStudy : chr [1:10] "SRP010483" "SRP010483" "SRP010483" "SRP010483" ...
## ..$ BioProject : chr [1:10] "PRJNA151601" "PRJNA151601" "PRJNA151601" "PRJNA151601" ...
## ..$ Study_Pubmed_id : int [1:10] 2 2 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:10] 151601 151601 151601 151601 151601 151601 151601 151601 151601 151601
## ..$ Sample : chr [1:10] "SRS290090" "SRS290091" "SRS290092" "SRS290093" ...
## ..$ BioSample : chr [1:10] "SAMN00778829" "SAMN00778830" "SAMN00778831" "SAMN00778832" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA049532" "SRA049532" "SRA049532" "SRA049532" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "B7E910C70FB0AE1C37106D61D5AEBCD6" "C7D73D56277DD61EBEA7949D25A5099D" "02E66D7D71FB32E98972C9FA6BD99970" "201A9D02EDD3F66E324E15B5BB58E08F" ...
## ..$ ReadHash : chr [1:10] "9267DAAA0DD36698D09CA4780DDAE451" "A11C10413C3A7574967498EF45CC0A93" "A1D6525B7420E5DBCA84A3D5DDA5FC69" "3EE8B8CD15590CA7A06FB34E413C0159" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP081574:Gene expression differentially regulated in CD8+ T cells stimulated with anti-CD3 and anti-CD28:Ctrl;SRX2018467,SRX2018468,SRX2018469,SRX2018470,SRX2018471,SRX2018472,SRX2018473,SRX2018474:StimUntreat; SRX2018475,SRX2018476,SRX2018477,SRX2018478,SRX2018479,SRX2018480,SRX2018481,SRX2018489,SRX2018490,SRX2018491,SRX2018492,SRX2018493,SRX2018494,SRX2018495,SRX2018501,SRX2018502,SRX2018503,SRX2018504,SRX2018505,SRX2018506,SRX2018507,SRX2018508,SRX2018509,SRX2018516,SRX2018517,SRX2018518,SRX2018519,SRX2018520,SRX2018522,SRX2018524## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 38 variables:
## ..$ SRR4026434: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026435: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026436: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026437: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026438: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026439: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026440: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026441: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026442: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026443: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026444: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026445: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026446: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026447: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026448: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026456: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026457: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026458: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026459: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026460: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026461: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026462: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026468: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026469: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026470: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026471: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026472: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026473: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026474: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026475: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026476: int [1:58302] 0 2 0 0 0 0 0 1 0 0 ...
## ..$ SRR4026483: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026484: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026485: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026486: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026487: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026489: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026491: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 38 variables:
## ..$ SRR4026434: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026435: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026436: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026437: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026438: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026439: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026440: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026441: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026442: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026443: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026444: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026445: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026446: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026447: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026448: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026456: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026457: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026458: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026459: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026460: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026461: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026462: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026468: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026469: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026470: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026471: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026472: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026473: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026474: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026475: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026476: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026483: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026484: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026485: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026486: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026487: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026489: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026491: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 38 variables:
## ..$ SRR4026434: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026435: chr [1:30] "SE" "Sanger/Illumina1.9" "37" "58" ...
## ..$ SRR4026436: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026437: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026438: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026439: chr [1:30] "SE" "Sanger/Illumina1.9" "39" "58" ...
## ..$ SRR4026440: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026441: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026442: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026443: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026444: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026445: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "58" ...
## ..$ SRR4026446: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026447: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026448: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026456: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026457: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026458: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026459: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026460: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "58" ...
## ..$ SRR4026461: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026462: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026468: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026469: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026470: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026471: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026472: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026473: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026474: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026475: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026476: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026483: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026484: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026485: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026486: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026487: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026489: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026491: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## $ MetadataSummary:'data.frame': 38 obs. of 7 variables:
## ..$ QC_summary : chr [1:38] "WARN(4,5,7)" "WARN(1,4,5,6,7,8)" "WARN(4,5,7)" "WARN(1,4,5,6,7)" ...
## ..$ SRX_accession: chr [1:38] "SRX2018467" "SRX2018468" "SRX2018469" "SRX2018470" ...
## ..$ SRS_accession: chr [1:38] "SRS1614372" "SRS1614373" "SRS1614371" "SRS1614370" ...
## ..$ SRP_accession: chr [1:38] "SRP081574" "SRP081574" "SRP081574" "SRP081574" ...
## ..$ Sample_name : chr [1:38] "GSM2274915" "GSM2274916" "GSM2274917" "GSM2274918" ...
## ..$ GEO_series : chr [1:38] "GSE85530" "GSE85530" "GSE85530" "GSE85530" ...
## ..$ Library_name : logi [1:38] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 38 obs. of 52 variables:
## ..$ QC_summary : chr [1:38] "WARN(4,5,7)" "WARN(1,4,5,6,7,8)" "WARN(4,5,7)" "WARN(1,4,5,6,7)" ...
## ..$ SRX_accession : chr [1:38] "SRX2018467" "SRX2018468" "SRX2018469" "SRX2018470" ...
## ..$ SRS_accession : chr [1:38] "SRS1614372" "SRS1614373" "SRS1614371" "SRS1614370" ...
## ..$ SRP_accession : chr [1:38] "SRP081574" "SRP081574" "SRP081574" "SRP081574" ...
## ..$ Sample_name : chr [1:38] "GSM2274915" "GSM2274916" "GSM2274917" "GSM2274918" ...
## ..$ GEO_series : chr [1:38] "GSE85530" "GSE85530" "GSE85530" "GSE85530" ...
## ..$ Library_name : logi [1:38] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:38] "GSM2274915" "GSM2274916" "GSM2274917" "GSM2274918" ...
## ..$ ReleaseDate : chr [1:38] "2016-11-21 10:13:58" "2016-11-21 10:13:58" "2016-11-21 10:13:58" "2016-11-21 10:13:58" ...
## ..$ LoadDate : chr [1:38] "2016-08-12 17:11:00" "2016-08-12 17:11:14" "2016-08-12 17:11:35" "2016-08-12 17:10:37" ...
## ..$ spots : int [1:38] 10553756 8302904 10420731 8433054 9569565 11260220 9925935 10690654 11411725 11636903 ...
## ..$ bases : int [1:38] 606716543 477227693 598688833 484341843 549976422 647086050 570522608 614665726 655934144 668734585 ...
## ..$ spots_with_mates : int [1:38] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:38] 57 57 57 57 57 57 57 57 57 57 ...
## ..$ size_MB : int [1:38] 211 168 209 169 192 225 198 214 229 235 ...
## ..$ AssemblyName : logi [1:38] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:38] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026434/SRR4026434.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026435/SRR4026435.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026436/SRR4026436.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026437/SRR4026437.1" ...
## ..$ LibraryName : logi [1:38] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:38] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:38] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:38] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:38] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:38] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:38] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:38] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:38] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:38] "SRP081574" "SRP081574" "SRP081574" "SRP081574" ...
## ..$ BioProject : chr [1:38] "PRJNA338796" "PRJNA338796" "PRJNA338796" "PRJNA338796" ...
## ..$ Study_Pubmed_id : logi [1:38] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:38] 338796 338796 338796 338796 338796 338796 338796 338796 338796 338796 ...
## ..$ Sample : chr [1:38] "SRS1614372" "SRS1614373" "SRS1614371" "SRS1614370" ...
## ..$ BioSample : chr [1:38] "SAMN05570956" "SAMN05570955" "SAMN05570954" "SAMN05570953" ...
## ..$ SampleType : chr [1:38] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:38] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:38] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:38] NA NA NA NA NA NA ...
## ..$ source : logi [1:38] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:38] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:38] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:38] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:38] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:38] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:38] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:38] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:38] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:38] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:38] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:38] "SRA452011" "SRA452011" "SRA452011" "SRA452011" ...
## ..$ dbgap_study_accession: logi [1:38] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:38] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:38] "CD914D32077DAE3F9F0E94AB6F802B64" "E046F348CF7C74BB1EE237F33B8EB641" "EAEDFDAFEB9C3C99F91E73294BB34902" "CAA5D7DE2FC5066A88C25C102B1F8012" ...
## ..$ ReadHash : chr [1:38] "0E714AB2F87CFA6AAA2967F6A5C5DE5A" "F572E2A436D6257F385383DB990E6CC8" "782E5B5FE934EAA2149C0D14CA573486" "D5F92C4F7928FEFD9925CBFADDBE79D5" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 46 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP081574:Gene expression differentially regulated in CD8+ T cells stimulated with anti-CD3 and anti-CD28 and PVR-Fc treatment:Ctrl;Ctrl;SRX2018467,SRX2018468,SRX2018469,SRX2018470,SRX2018471,SRX2018472,SRX2018473,SRX2018474:StimTreat; SRX2018482,SRX2018483,SRX2018484,SRX2018485,SRX2018486,SRX2018487,SRX2018488,SRX2018496,SRX2018497,SRX2018498,SRX2018499, SRX2018510,SRX2018511,SRX2018512,SRX2018513,SRX2018514,SRX2018515,SRX2018521,SRX2018523,SRX2018525,SRX2018526,SRX2018527,SRX2018528,SRX2018529## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 24 variables:
## ..$ SRR4026449: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026450: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026451: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026452: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026453: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026454: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026455: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026463: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026464: int [1:58302] 0 0 0 0 0 0 0 1 0 0 ...
## ..$ SRR4026465: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026466: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026477: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026478: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026479: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026480: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026481: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026482: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026488: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026490: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026492: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026493: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026494: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026495: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026496: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 24 variables:
## ..$ SRR4026449: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026450: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026451: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026452: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026453: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026454: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026455: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026463: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026464: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026465: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026466: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026477: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026478: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026479: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026480: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026481: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026482: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026488: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026490: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026492: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026493: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026494: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026495: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026496: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 24 variables:
## ..$ SRR4026449: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026450: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026451: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026452: chr [1:30] "SE" "Sanger/Illumina1.9" "39" "58" ...
## ..$ SRR4026453: chr [1:30] "SE" "Sanger/Illumina1.9" "37" "58" ...
## ..$ SRR4026454: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026455: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026463: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026464: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026465: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026466: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026477: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026478: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026479: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026480: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026481: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026482: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026488: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026490: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026492: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026493: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026494: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026495: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026496: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## $ MetadataSummary:'data.frame': 24 obs. of 7 variables:
## ..$ QC_summary : chr [1:24] "WARN(5,7)" "WARN(5,7)" "WARN(1,5,7)" "WARN(5,7)" ...
## ..$ SRX_accession: chr [1:24] "SRX2018482" "SRX2018483" "SRX2018484" "SRX2018485" ...
## ..$ SRS_accession: chr [1:24] "SRS1614384" "SRS1614386" "SRS1614387" "SRS1614390" ...
## ..$ SRP_accession: chr [1:24] "SRP081574" "SRP081574" "SRP081574" "SRP081574" ...
## ..$ Sample_name : chr [1:24] "GSM2274930" "GSM2274931" "GSM2274932" "GSM2274933" ...
## ..$ GEO_series : chr [1:24] "GSE85530" "GSE85530" "GSE85530" "GSE85530" ...
## ..$ Library_name : logi [1:24] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 24 obs. of 52 variables:
## ..$ QC_summary : chr [1:24] "WARN(5,7)" "WARN(5,7)" "WARN(1,5,7)" "WARN(5,7)" ...
## ..$ SRX_accession : chr [1:24] "SRX2018482" "SRX2018483" "SRX2018484" "SRX2018485" ...
## ..$ SRS_accession : chr [1:24] "SRS1614384" "SRS1614386" "SRS1614387" "SRS1614390" ...
## ..$ SRP_accession : chr [1:24] "SRP081574" "SRP081574" "SRP081574" "SRP081574" ...
## ..$ Sample_name : chr [1:24] "GSM2274930" "GSM2274931" "GSM2274932" "GSM2274933" ...
## ..$ GEO_series : chr [1:24] "GSE85530" "GSE85530" "GSE85530" "GSE85530" ...
## ..$ Library_name : logi [1:24] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:24] "GSM2274930" "GSM2274931" "GSM2274932" "GSM2274933" ...
## ..$ ReleaseDate : chr [1:24] "2016-11-21 10:13:58" "2016-11-21 10:13:58" "2016-11-21 10:13:58" "2016-11-21 10:13:58" ...
## ..$ LoadDate : chr [1:24] "2016-08-12 17:12:11" "2016-08-12 17:12:54" "2016-08-12 17:11:46" "2016-08-12 17:13:39" ...
## ..$ spots : int [1:24] 11798170 12165361 8940912 10662543 10630171 12868640 11262869 11150504 14003766 13668571 ...
## ..$ bases : int [1:24] 678341067 699440376 514146028 612969635 610944451 739838662 647409730 640829258 804981961 785851760 ...
## ..$ spots_with_mates : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:24] 57 57 57 57 57 57 57 57 57 57 ...
## ..$ size_MB : int [1:24] 237 245 219 214 248 261 226 223 281 274 ...
## ..$ AssemblyName : logi [1:24] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:24] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026449/SRR4026449.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026450/SRR4026450.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026451/SRR4026451.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026452/SRR4026452.1" ...
## ..$ LibraryName : logi [1:24] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:24] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:24] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:24] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:24] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:24] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:24] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:24] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:24] "SRP081574" "SRP081574" "SRP081574" "SRP081574" ...
## ..$ BioProject : chr [1:24] "PRJNA338796" "PRJNA338796" "PRJNA338796" "PRJNA338796" ...
## ..$ Study_Pubmed_id : logi [1:24] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:24] 338796 338796 338796 338796 338796 338796 338796 338796 338796 338796 ...
## ..$ Sample : chr [1:24] "SRS1614384" "SRS1614386" "SRS1614387" "SRS1614390" ...
## ..$ BioSample : chr [1:24] "SAMN05571035" "SAMN05571034" "SAMN05571029" "SAMN05571028" ...
## ..$ SampleType : chr [1:24] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:24] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:24] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:24] NA NA NA NA NA NA ...
## ..$ source : logi [1:24] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:24] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:24] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:24] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:24] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:24] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:24] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:24] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:24] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:24] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:24] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:24] "SRA452011" "SRA452011" "SRA452011" "SRA452011" ...
## ..$ dbgap_study_accession: logi [1:24] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:24] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:24] "8C687A96C5A0959BF6EFD3A5E89FEBF2" "0F86C0E34588030BEE923EADBE9DC4C4" "7F9D9309B36D869F9DA69DFF80C19818" "FD9E56F6EDCE18932A65AA281381A266" ...
## ..$ ReadHash : chr [1:24] "9D0C0580E31AC07A6E4EADC180F263B3" "6B680377797386F6B44F81BC3E803B1B" "948343B972D7E0D01879C8B5FFAD7D84" "89444C9C9E961CBED4CEB78033DA7278" ...
## $ absent : chr(0)## SRP081574:Gene expression differentially regulated in CD8+ T cells stimulated with anti-CD3 and anti-CD28 vs anti-CD3 and anti-CD28 and PVR-Fc treatment:StimUntreat; SRX2018475,SRX2018476,SRX2018477,SRX2018478,SRX2018479,SRX2018480,SRX2018481,SRX2018489,SRX2018490,SRX2018491,SRX2018492,SRX2018493,SRX2018494,SRX2018495,SRX2018501,SRX2018502,SRX2018503,SRX2018504,SRX2018505,SRX2018506,SRX2018507,SRX2018508,SRX2018509,SRX2018516,SRX2018517,SRX2018518,SRX2018519,SRX2018520,SRX2018522,SRX2018524:StimTreat; SRX2018482,SRX2018483,SRX2018484,SRX2018485,SRX2018486,SRX2018487,SRX2018488,SRX2018496,SRX2018497,SRX2018498,SRX2018499, SRX2018510,SRX2018511,SRX2018512,SRX2018513,SRX2018514,SRX2018515,SRX2018521,SRX2018523,SRX2018525,SRX2018526,SRX2018527,SRX2018528,SRX2018529
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 53 variables:
## ..$ SRR4026442: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026443: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026444: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026445: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026446: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026447: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026448: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026449: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026450: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026451: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026452: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026453: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026454: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026455: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026456: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026457: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026458: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026459: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026460: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026461: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026462: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026463: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026464: int [1:58302] 0 0 0 0 0 0 0 1 0 0 ...
## ..$ SRR4026465: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026466: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026468: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026469: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026470: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026471: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026472: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026473: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026474: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026475: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026476: int [1:58302] 0 2 0 0 0 0 0 1 0 0 ...
## ..$ SRR4026478: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026479: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026480: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026481: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026482: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026483: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026484: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026485: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026486: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026487: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026488: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026489: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026490: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026491: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026492: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026493: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026494: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026495: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026496: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 53 variables:
## ..$ SRR4026442: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026443: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026444: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026445: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026446: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026447: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026448: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026449: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026450: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026451: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026452: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026453: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026454: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026455: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026456: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026457: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026458: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026459: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026460: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026461: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026462: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026463: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026464: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026465: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026466: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026468: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026469: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026470: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026471: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026472: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026473: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026474: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026475: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026476: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026478: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026479: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026480: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026481: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026482: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026483: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026484: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026485: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026486: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026487: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026488: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026489: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026490: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026491: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026492: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026493: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026494: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026495: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026496: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 53 variables:
## ..$ SRR4026442: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026443: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026444: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026445: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "58" ...
## ..$ SRR4026446: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026447: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026448: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026449: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026450: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026451: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026452: chr [1:30] "SE" "Sanger/Illumina1.9" "39" "58" ...
## ..$ SRR4026453: chr [1:30] "SE" "Sanger/Illumina1.9" "37" "58" ...
## ..$ SRR4026454: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026455: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026456: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026457: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026458: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026459: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026460: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "58" ...
## ..$ SRR4026461: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026462: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026463: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026464: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026465: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026466: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "58" ...
## ..$ SRR4026468: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026469: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026470: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026471: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026472: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026473: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026474: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026475: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026476: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026478: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026479: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026480: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026481: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026482: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026483: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026484: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026485: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026486: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026487: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026488: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026489: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026490: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026491: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026492: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026493: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026494: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026495: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## ..$ SRR4026496: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "57" ...
## $ MetadataSummary:'data.frame': 53 obs. of 7 variables:
## ..$ QC_summary : chr [1:53] "WARN(5,7)" "WARN(5)" "WARN(5,7)" "WARN(1,4,5,7)" ...
## ..$ SRX_accession: chr [1:53] "SRX2018475" "SRX2018476" "SRX2018477" "SRX2018478" ...
## ..$ SRS_accession: chr [1:53] "SRS1614378" "SRS1614380" "SRS1614379" "SRS1614381" ...
## ..$ SRP_accession: chr [1:53] "SRP081574" "SRP081574" "SRP081574" "SRP081574" ...
## ..$ Sample_name : chr [1:53] "GSM2274923" "GSM2274924" "GSM2274925" "GSM2274926" ...
## ..$ GEO_series : chr [1:53] "GSE85530" "GSE85530" "GSE85530" "GSE85530" ...
## ..$ Library_name : logi [1:53] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 53 obs. of 52 variables:
## ..$ QC_summary : chr [1:53] "WARN(5,7)" "WARN(5)" "WARN(5,7)" "WARN(1,4,5,7)" ...
## ..$ SRX_accession : chr [1:53] "SRX2018475" "SRX2018476" "SRX2018477" "SRX2018478" ...
## ..$ SRS_accession : chr [1:53] "SRS1614378" "SRS1614380" "SRS1614379" "SRS1614381" ...
## ..$ SRP_accession : chr [1:53] "SRP081574" "SRP081574" "SRP081574" "SRP081574" ...
## ..$ Sample_name : chr [1:53] "GSM2274923" "GSM2274924" "GSM2274925" "GSM2274926" ...
## ..$ GEO_series : chr [1:53] "GSE85530" "GSE85530" "GSE85530" "GSE85530" ...
## ..$ Library_name : logi [1:53] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:53] "GSM2274923" "GSM2274924" "GSM2274925" "GSM2274926" ...
## ..$ ReleaseDate : chr [1:53] "2016-11-21 10:13:58" "2016-11-21 10:13:58" "2016-11-21 10:13:58" "2016-11-21 10:13:58" ...
## ..$ LoadDate : chr [1:53] "2016-08-12 17:11:39" "2016-08-12 17:12:40" "2016-08-12 17:13:12" "2016-08-12 17:11:24" ...
## ..$ spots : int [1:53] 11411725 11636903 11043952 7712344 10855466 11572637 10954349 11798170 12165361 8940912 ...
## ..$ bases : int [1:53] 655934144 668734585 634794868 443256883 624032548 665179171 629592201 678341067 699440376 514146028 ...
## ..$ spots_with_mates : int [1:53] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:53] 57 57 57 57 57 57 57 57 57 57 ...
## ..$ size_MB : int [1:53] 229 235 222 187 232 232 220 237 245 219 ...
## ..$ AssemblyName : logi [1:53] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:53] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026442/SRR4026442.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026443/SRR4026443.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026444/SRR4026444.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026445/SRR4026445.1" ...
## ..$ LibraryName : logi [1:53] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:53] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:53] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:53] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:53] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:53] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:53] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:53] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:53] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:53] "SRP081574" "SRP081574" "SRP081574" "SRP081574" ...
## ..$ BioProject : chr [1:53] "PRJNA338796" "PRJNA338796" "PRJNA338796" "PRJNA338796" ...
## ..$ Study_Pubmed_id : logi [1:53] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:53] 338796 338796 338796 338796 338796 338796 338796 338796 338796 338796 ...
## ..$ Sample : chr [1:53] "SRS1614378" "SRS1614380" "SRS1614379" "SRS1614381" ...
## ..$ BioSample : chr [1:53] "SAMN05570948" "SAMN05571037" "SAMN05571036" "SAMN05571033" ...
## ..$ SampleType : chr [1:53] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:53] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:53] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:53] NA NA NA NA NA NA ...
## ..$ source : logi [1:53] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:53] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:53] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:53] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:53] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:53] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:53] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:53] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:53] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:53] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:53] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:53] "SRA452011" "SRA452011" "SRA452011" "SRA452011" ...
## ..$ dbgap_study_accession: logi [1:53] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:53] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:53] "D8B09D43E8B94BA80CA2300DF292927F" "AF325853B73EC5272E0A4A05E5180E07" "E5A8A46BBDA79B1B0761EB07D41B321B" "5A25767A40F56B7E08BEA812C9852D8E" ...
## ..$ ReadHash : chr [1:53] "4CFE23262EB9142C86A64E6AE09E2085" "181CA1C8B63C7C40C28B1E8D4C447AC5" "370B176B7DDE20FCC60010EB1FFA6EB6" "1CFCF506274B5A3783489857AE500958" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 40 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP087720:Gene expression differentially regulated in human islets by Asf1B overexpression:Ctrl; SRX2153424,SRX2153425,SRX2153426,SRX2153427,SRX2153428,SRX2153429,SRX2153430,SRX2153431,SRX2153432,SRX2153433:Asf1B; SRX2153434,SRX2153435,SRX2153436,SRX2153437,SRX2153438,SRX2153439,SRX2153440,SRX2153441,SRX2153442,SRX2153443## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 20 variables:
## ..$ SRR4213103: int [1:58302] 0 0 3 0 0 0 0 0 0 2 ...
## ..$ SRR4213104: int [1:58302] 0 1 4 0 0 0 0 0 0 0 ...
## ..$ SRR4213105: int [1:58302] 0 5 6 0 0 0 0 0 0 0 ...
## ..$ SRR4213106: int [1:58302] 0 4 6 0 0 0 0 0 0 0 ...
## ..$ SRR4213107: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR4213108: int [1:58302] 0 3 6 0 0 0 0 0 0 1 ...
## ..$ SRR4213109: int [1:58302] 0 1 10 0 0 0 0 0 0 2 ...
## ..$ SRR4213110: int [1:58302] 0 0 7 1 0 0 0 0 0 0 ...
## ..$ SRR4213111: int [1:58302] 0 0 6 0 0 0 0 0 0 0 ...
## ..$ SRR4213112: int [1:58302] 0 0 4 0 0 0 0 0 0 0 ...
## ..$ SRR4213113: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR4213114: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR4213115: int [1:58302] 0 3 6 0 0 0 0 0 0 0 ...
## ..$ SRR4213116: int [1:58302] 1 4 2 0 0 0 0 0 0 3 ...
## ..$ SRR4213117: int [1:58302] 1 1 4 0 0 0 0 0 0 2 ...
## ..$ SRR4213118: int [1:58302] 0 1 7 0 0 0 0 0 0 1 ...
## ..$ SRR4213119: int [1:58302] 0 0 4 0 0 0 0 0 0 3 ...
## ..$ SRR4213120: int [1:58302] 0 3 4 0 0 0 0 0 0 0 ...
## ..$ SRR4213121: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR4213122: int [1:58302] 0 5 6 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 20 variables:
## ..$ SRR4213103: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213104: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213105: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213106: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213107: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213108: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213109: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213110: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213111: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213112: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213113: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213114: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213115: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213116: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213117: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213118: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213119: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213120: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213121: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4213122: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 20 variables:
## ..$ SRR4213103: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213104: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213105: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213106: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213107: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213108: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213109: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213110: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213111: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213112: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213113: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213114: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213115: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213116: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213117: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213118: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213119: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213120: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213121: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4213122: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 20 obs. of 7 variables:
## ..$ QC_summary : chr [1:20] "WARN(8)" "PASS" "PASS" "WARN(8)" ...
## ..$ SRX_accession: chr [1:20] "SRX2153424" "SRX2153425" "SRX2153426" "SRX2153427" ...
## ..$ SRS_accession: chr [1:20] "SRS1683936" "SRS1683937" "SRS1683938" "SRS1683940" ...
## ..$ SRP_accession: chr [1:20] "SRP087720" "SRP087720" "SRP087720" "SRP087720" ...
## ..$ Sample_name : chr [1:20] "GSM2306833" "GSM2306834" "GSM2306835" "GSM2306836" ...
## ..$ GEO_series : chr [1:20] "GSE86611" "GSE86611" "GSE86611" "GSE86611" ...
## ..$ Library_name : logi [1:20] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 20 obs. of 52 variables:
## ..$ QC_summary : chr [1:20] "WARN(8)" "PASS" "PASS" "WARN(8)" ...
## ..$ SRX_accession : chr [1:20] "SRX2153424" "SRX2153425" "SRX2153426" "SRX2153427" ...
## ..$ SRS_accession : chr [1:20] "SRS1683936" "SRS1683937" "SRS1683938" "SRS1683940" ...
## ..$ SRP_accession : chr [1:20] "SRP087720" "SRP087720" "SRP087720" "SRP087720" ...
## ..$ Sample_name : chr [1:20] "GSM2306833" "GSM2306834" "GSM2306835" "GSM2306836" ...
## ..$ GEO_series : chr [1:20] "GSE86611" "GSE86611" "GSE86611" "GSE86611" ...
## ..$ Library_name : logi [1:20] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:20] "GSM2306833" "GSM2306834" "GSM2306835" "GSM2306836" ...
## ..$ ReleaseDate : chr [1:20] "2016-09-15 16:09:38" "2016-09-15 16:09:38" "2016-09-15 16:09:38" "2016-09-15 16:09:38" ...
## ..$ LoadDate : chr [1:20] "2016-09-09 11:12:05" "2016-09-09 11:10:12" "2016-09-09 11:12:58" "2016-09-09 11:12:57" ...
## ..$ spots : int [1:20] 19608036 17518819 24305194 18320055 21699864 20328926 24233482 23992147 14471188 14783535 ...
## ..$ bases : num [1:20] 1.98e+09 1.77e+09 2.45e+09 1.85e+09 2.19e+09 ...
## ..$ spots_with_mates : int [1:20] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:20] 101 101 101 101 101 101 101 101 101 101 ...
## ..$ size_MB : int [1:20] 1381 1236 1709 1292 1531 1435 1702 1687 1020 1042 ...
## ..$ AssemblyName : logi [1:20] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:20] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR4213103/SRR4213103.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR4213104/SRR4213104.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR4213105/SRR4213105.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR4213106/SRR4213106.1" ...
## ..$ LibraryName : logi [1:20] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:20] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:20] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:20] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:20] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:20] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:20] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:20] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:20] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:20] "SRP087720" "SRP087720" "SRP087720" "SRP087720" ...
## ..$ BioProject : chr [1:20] "PRJNA342403" "PRJNA342403" "PRJNA342403" "PRJNA342403" ...
## ..$ Study_Pubmed_id : logi [1:20] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:20] 342403 342403 342403 342403 342403 342403 342403 342403 342403 342403 ...
## ..$ Sample : chr [1:20] "SRS1683936" "SRS1683937" "SRS1683938" "SRS1683940" ...
## ..$ BioSample : chr [1:20] "SAMN05756325" "SAMN05756324" "SAMN05756323" "SAMN05756321" ...
## ..$ SampleType : chr [1:20] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:20] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:20] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:20] NA NA NA NA NA NA ...
## ..$ source : logi [1:20] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:20] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:20] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:20] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:20] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:20] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:20] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:20] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:20] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:20] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:20] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:20] "SRA465393" "SRA465393" "SRA465393" "SRA465393" ...
## ..$ dbgap_study_accession: logi [1:20] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:20] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:20] "18C125AC0705D97C3B67B4BD1A32340D" "5D3A1FE7B8A9F17A9DB26CC057C81940" "7678B7704ED8C340D56DC922A6D46CEC" "BD1855D0649769D2B7CD1FBE73916E5B" ...
## ..$ ReadHash : chr [1:20] "D124A746F435F2DBA6831840501250C6" "1355322793DFAA034840BF99C38431E1" "53145A686672675D38057BF0731A6395" "E17ABD533FE048BB0B499154BCD14DEF" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 153 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP093728:Genes expression differentially regulated in type 2 diabetic human serum samples:Ctrl;SRX2359251,SRX2359252,SRX2359253,SRX2359254,SRX2359255,SRX2359256,SRX2359257,SRX2359258,SRX2359268,SRX2359269,SRX2359270,SRX2359271,SRX2359272,SRX2359273,SRX2359274,SRX2359275:T2DM;SRX2359235,SRX2359236,SRX2359237,SRX2359238,SRX2359239,SRX2359240,SRX2359241## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 23 variables:
## ..$ SRR5034616: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034617: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034618: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034619: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034620: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034621: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034622: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034632: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034633: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034634: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034635: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034636: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034637: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034638: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034639: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034649: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034650: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034651: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034652: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034653: int [1:58302] 0 0 0 0 0 0 0 0 0 2 ...
## ..$ SRR5034654: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034655: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034656: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 23 variables:
## ..$ SRR5034616: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034617: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034618: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034619: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034620: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034621: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034622: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034632: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034633: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034634: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034635: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034636: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034637: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034638: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034639: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034649: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034650: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034651: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034652: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034653: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034654: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034655: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5034656: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 23 variables:
## ..$ SRR5034616: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034617: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034618: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034619: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034620: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034621: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034622: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034632: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034633: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034634: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034635: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034636: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034637: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034638: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034639: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034649: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034650: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034651: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034652: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034653: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034654: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034655: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## ..$ SRR5034656: chr [1:30] "SE" "Sanger/Illumina1.9" "99" "99" ...
## $ MetadataSummary:'data.frame': 23 obs. of 7 variables:
## ..$ QC_summary : chr [1:23] "FAIL(3,4,5,6,7)" "FAIL(3,4)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6)" ...
## ..$ SRX_accession: chr [1:23] "SRX2359235" "SRX2359236" "SRX2359237" "SRX2359238" ...
## ..$ SRS_accession: chr [1:23] "SRS1807882" "SRS1807883" "SRS1807884" "SRS1807885" ...
## ..$ SRP_accession: chr [1:23] "SRP093728" "SRP093728" "SRP093728" "SRP093728" ...
## ..$ Sample_name : chr [1:23] "GSM2395951" "GSM2395952" "GSM2395953" "GSM2395954" ...
## ..$ GEO_series : chr [1:23] "GSE90028" "GSE90028" "GSE90028" "GSE90028" ...
## ..$ Library_name : logi [1:23] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 23 obs. of 52 variables:
## ..$ QC_summary : chr [1:23] "FAIL(3,4,5,6,7)" "FAIL(3,4)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6)" ...
## ..$ SRX_accession : chr [1:23] "SRX2359235" "SRX2359236" "SRX2359237" "SRX2359238" ...
## ..$ SRS_accession : chr [1:23] "SRS1807882" "SRS1807883" "SRS1807884" "SRS1807885" ...
## ..$ SRP_accession : chr [1:23] "SRP093728" "SRP093728" "SRP093728" "SRP093728" ...
## ..$ Sample_name : chr [1:23] "GSM2395951" "GSM2395952" "GSM2395953" "GSM2395954" ...
## ..$ GEO_series : chr [1:23] "GSE90028" "GSE90028" "GSE90028" "GSE90028" ...
## ..$ Library_name : logi [1:23] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:23] "GSM2395951" "GSM2395952" "GSM2395953" "GSM2395954" ...
## ..$ ReleaseDate : chr [1:23] "2017-06-09 16:20:35" "2017-06-09 16:20:35" "2017-06-09 16:20:35" "2017-06-09 16:20:35" ...
## ..$ LoadDate : chr [1:23] "2016-11-18 09:22:14" "2016-11-18 09:52:16" "2016-11-18 09:38:48" "2016-11-18 09:27:38" ...
## ..$ spots : int [1:23] 10680752 112175148 49863461 16676715 12705671 25795128 56362314 6179023 10528310 4445188 ...
## ..$ bases : num [1:23] 1.06e+09 1.11e+10 4.94e+09 1.65e+09 1.26e+09 ...
## ..$ spots_with_mates : int [1:23] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:23] 99 99 99 99 99 99 99 99 99 99 ...
## ..$ size_MB : int [1:23] 760 7687 3359 1220 913 1812 3811 457 792 327 ...
## ..$ AssemblyName : logi [1:23] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:23] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR5034616/SRR5034616.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5034617/SRR5034617.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5034618/SRR5034618.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5034619/SRR5034619.1" ...
## ..$ LibraryName : logi [1:23] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:23] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" ...
## ..$ LibrarySelection : chr [1:23] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ LibrarySource : chr [1:23] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:23] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:23] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:23] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:23] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:23] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:23] "SRP093728" "SRP093728" "SRP093728" "SRP093728" ...
## ..$ BioProject : chr [1:23] "PRJNA354381" "PRJNA354381" "PRJNA354381" "PRJNA354381" ...
## ..$ Study_Pubmed_id : int [1:23] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:23] 354381 354381 354381 354381 354381 354381 354381 354381 354381 354381 ...
## ..$ Sample : chr [1:23] "SRS1807882" "SRS1807883" "SRS1807884" "SRS1807885" ...
## ..$ BioSample : chr [1:23] "SAMN06036024" "SAMN06036071" "SAMN06036070" "SAMN06036069" ...
## ..$ SampleType : chr [1:23] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:23] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:23] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:23] NA NA NA NA NA NA ...
## ..$ source : logi [1:23] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:23] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:23] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:23] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:23] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:23] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:23] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:23] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:23] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:23] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:23] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:23] "SRA496232" "SRA496232" "SRA496232" "SRA496232" ...
## ..$ dbgap_study_accession: logi [1:23] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:23] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:23] "4D88D3DFFA1DF0439E0479326EA5CAAF" "AB8EC79667CF45DF037E22EC13AA672D" "F54E4034D5805DC363F422E9472F2C9B" "CA0F396EE6BEA8BD64BF0AB404EF5098" ...
## ..$ ReadHash : chr [1:23] "675796A4987426C069ABDF94EFA9A3CE" "B26DAC9BADCF6DADC0D7F0F88767A069" "9A7B842ACA5252E02CEC45D122807FC1" "10E05B6E57606647D8EA69C83A1573C7" ...
## $ absent : chr(0)## SRP103811:alpha cells versus beta cells from three East-Asian non-diabetic subjects:alpha;SRX2733099,SRX2733104,SRX2733110,SRX2733111,SRX2733112,SRX2733113,SRX2733115,SRX2733117,SRX2733119,SRX2733123,SRX2733126,SRX2733128,SRX2733130,SRX2733132,SRX2733133,SRX2733135,SRX2733140,SRX2733141,SRX2733143,SRX2733146,SRX2733147,SRX2733149,SRX2733150,SRX2733151,SRX2733153,SRX2733156,SRX2733157,SRX2733158,SRX2733159,SRX2733160,SRX2733161,SRX2733162,SRX2733163,SRX2733164,SRX2733170,SRX2733177,SRX2733180,SRX2733183,SRX2733184,SRX2733187,SRX2733189,SRX2733190,SRX2733191,SRX2733192,SRX2733205,SRX2733206,SRX2733210,SRX2733211,SRX2733212,SRX2733212,SRX2733213,SRX2733213,SRX2733215,SRX2733215,SRX2733216,SRX2733216,SRX2733217,SRX2733217,SRX2733218,SRX2733218,SRX2733221,SRX2733221,SRX2733222,SRX2733222,SRX2733223,SRX2733223,SRX2733224,SRX2733224,SRX2733225,SRX2733225,SRX2733228,SRX2733228,SRX2733229,SRX2733229,SRX2733231,SRX2733231,SRX2733232,SRX2733232,SRX2733233,SRX2733233,SRX2733234,SRX2733234,SRX2733235,SRX2733235,SRX2733237,SRX2733237,SRX2733238,SRX2733238,SRX2733243,SRX2733243,SRX2733247,SRX2733247,SRX2733248,SRX2733248,SRX2733249,SRX2733249,SRX2733250,SRX2733250,SRX2733251,SRX2733251,SRX2733252,SRX2733252,SRX2733253,SRX2733253,SRX2733255,SRX2733255,SRX2733256,SRX2733256,SRX2733257,SRX2733257,SRX2733258,SRX2733258,SRX2733259,SRX2733259,SRX2733260,SRX2733260,SRX2733261,SRX2733261,SRX2733262,SRX2733262,SRX2733263,SRX2733263,SRX2733264,SRX2733264,SRX2733265,SRX2733265,SRX2733266,SRX2733266,SRX2733268,SRX2733268,SRX2733269,SRX2733269,SRX2733270,SRX2733270,SRX2733271,SRX2733271,SRX2733272,SRX2733272,SRX2733273,SRX2733273,SRX2733274,SRX2733274,SRX2733275,SRX2733275,SRX2733276,SRX2733276,SRX2733277,SRX2733277,SRX2733278,SRX2733278,SRX2733279,SRX2733279,SRX2733280,SRX2733280,SRX2733281,SRX2733281,SRX2733282,SRX2733282,SRX2733283,SRX2733283,SRX2733285,SRX2733285,SRX2733286,SRX2733286,SRX2733287,SRX2733287,SRX2733289,SRX2733289,SRX2733290,SRX2733290,SRX2733291,SRX2733291,SRX2733292,SRX2733292,SRX2733293,SRX2733293,SRX2733294,SRX2733294,SRX2733295,SRX2733295,SRX2733303,SRX2733303,SRX2733305,SRX2733305,SRX2733316,SRX2733316,SRX2733317,SRX2733317:beta;SRX2733100,SRX2733101,SRX2733102,SRX2733103,SRX2733105,SRX2733106,SRX2733107,SRX2733108,SRX2733109,SRX2733114,SRX2733116,SRX2733118,SRX2733120,SRX2733121,SRX2733122,SRX2733124,SRX2733125,SRX2733127,SRX2733129,SRX2733131,SRX2733134,SRX2733136,SRX2733137,SRX2733138,SRX2733139,SRX2733142,SRX2733144,SRX2733145,SRX2733148,SRX2733152,SRX2733154,SRX2733155,SRX2733165,SRX2733166,SRX2733167,SRX2733168,SRX2733169,SRX2733171,SRX2733172,SRX2733173,SRX2733174,SRX2733175,SRX2733176,SRX2733178,SRX2733179,SRX2733181,SRX2733182,SRX2733185,SRX2733186,SRX2733188,SRX2733193,SRX2733194,SRX2733195,SRX2733196,SRX2733197,SRX2733198,SRX2733199,SRX2733200,SRX2733201,SRX2733202,SRX2733203,SRX2733204,SRX2733207,SRX2733208,SRX2733209,SRX2733214,SRX2733214,SRX2733219,SRX2733219,SRX2733220,SRX2733220,SRX2733226,SRX2733226,SRX2733227,SRX2733227,SRX2733230,SRX2733230,SRX2733236,SRX2733236,SRX2733239,SRX2733239,SRX2733240,SRX2733240,SRX2733241,SRX2733241,SRX2733242,SRX2733242,SRX2733244,SRX2733244,SRX2733245,SRX2733245,SRX2733246,SRX2733246,SRX2733254,SRX2733254,SRX2733267,SRX2733267,SRX2733284,SRX2733284,SRX2733288,SRX2733288,SRX2733296,SRX2733296,SRX2733297,SRX2733297,SRX2733298,SRX2733298,SRX2733299,SRX2733299,SRX2733300,SRX2733300,SRX2733301,SRX2733301,SRX2733302,SRX2733302,SRX2733304,SRX2733304,SRX2733306,SRX2733306,SRX2733307,SRX2733307,SRX2733308,SRX2733308,SRX2733309,SRX2733309,SRX2733310,SRX2733310,SRX2733311,SRX2733311,SRX2733312,SRX2733312,SRX2733313,SRX2733313,SRX2733314,SRX2733314,SRX2733315,SRX2733315,SRX2733318,SRX2733318,SRX2733319,SRX2733319,SRX2733320,SRX2733320,SRX2733321,SRX2733321;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 333 variables:
## ..$ SRR5443791: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443792: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443793: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443794: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443795: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443796: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443797: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443798: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443799: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443800: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443801: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443802: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443803: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443804: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443805: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443806: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443807: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443808: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443809: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443810: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443811: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443812: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443813: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443814: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443815: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443816: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443817: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443818: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443819: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443820: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443821: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443822: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443823: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443824: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443825: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443826: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443827: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443828: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443829: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443830: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443831: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443832: int [1:58302] 0 0 0 0 0 0 0 349 0 0 ...
## ..$ SRR5443833: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443834: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443835: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443836: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443837: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443838: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443839: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443840: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443841: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443842: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443843: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443844: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443845: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443846: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443847: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443848: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443849: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443850: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443851: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443852: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443853: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443854: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443855: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443856: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443857: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443858: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443859: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443860: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443861: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443862: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443863: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443864: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443865: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443866: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443867: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443868: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443869: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443870: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443871: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443872: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443873: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443874: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443875: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443876: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443877: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443878: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443879: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443880: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443881: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443882: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443883: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443884: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443885: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443886: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443887: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443888: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443889: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## .. [list output truncated]
## $ TxCounts :'data.frame': 180869 obs. of 333 variables:
## ..$ SRR5443791: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443792: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443793: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443794: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443795: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443796: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443797: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443798: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443799: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443800: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443801: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443802: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443803: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443804: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443805: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443806: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443807: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443808: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443809: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443810: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443811: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443812: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443813: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443814: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443815: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443816: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443817: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443818: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443819: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443820: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443821: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443822: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443823: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443824: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443825: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443826: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443827: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443828: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443829: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443830: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443831: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443832: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443833: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443834: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443835: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443836: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443837: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443838: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443839: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443840: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443841: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443842: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443843: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443844: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443845: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443846: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443847: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443848: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443849: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443850: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443851: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443852: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443853: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443854: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443855: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443856: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443857: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443858: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443859: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443860: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443861: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443862: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443863: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443864: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443865: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443866: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443867: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443868: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443869: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443870: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443871: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443872: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443873: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443874: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443875: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443876: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443877: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443878: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443879: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443880: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443881: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443882: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443883: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443884: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443885: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443886: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443887: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443888: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5443889: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## .. [list output truncated]
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 333 variables:
## ..$ SRR5443791: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443792: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443793: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443794: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443795: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443796: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443797: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443798: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443799: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443800: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443801: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443802: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443803: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443804: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443805: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443806: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443807: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443808: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443809: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443810: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443811: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443812: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443813: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443814: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443815: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443816: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443817: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443818: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443819: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443820: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443821: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443822: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443823: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443824: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443825: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443826: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443827: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443828: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443829: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443830: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443831: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443832: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443833: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443834: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443835: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443836: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443837: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443838: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443839: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443840: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443841: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443842: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443843: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443844: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443845: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443846: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443847: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443848: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443849: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443850: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443851: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443852: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443853: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443854: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443855: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443856: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443857: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443858: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443859: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443860: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443861: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443862: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443863: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443864: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443865: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443866: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443867: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443868: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443869: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443870: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443871: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443872: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443873: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443874: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443875: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443876: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443877: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443878: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443879: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443880: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443881: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443882: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443883: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443884: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443885: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443886: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443887: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443888: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## ..$ SRR5443889: chr [1:30] "PE" "Sanger/Illumina1.9" "140" "140" ...
## .. [list output truncated]
## $ MetadataSummary:'data.frame': 333 obs. of 7 variables:
## ..$ QC_summary : chr [1:333] "WARN(1,4,5,6,7,8)" "WARN(4,5,6,7)" "WARN(1,5,7)" "WARN(1,4,5,6,7)" ...
## ..$ SRX_accession: chr [1:333] "SRX2733099" "SRX2733100" "SRX2733101" "SRX2733102" ...
## ..$ SRS_accession: chr [1:333] "SRS2120997" "SRS2120999" "SRS2120998" "SRS2121000" ...
## ..$ SRP_accession: chr [1:333] "SRP103811" "SRP103811" "SRP103811" "SRP103811" ...
## ..$ Sample_name : chr [1:333] "GSM2574469" "GSM2574470" "GSM2574471" "GSM2574472" ...
## ..$ GEO_series : chr [1:333] "GSE97655" "GSE97655" "GSE97655" "GSE97655" ...
## ..$ Library_name : logi [1:333] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 333 obs. of 52 variables:
## ..$ QC_summary : chr [1:333] "WARN(1,4,5,6,7,8)" "WARN(4,5,6,7)" "WARN(1,5,7)" "WARN(1,4,5,6,7)" ...
## ..$ SRX_accession : chr [1:333] "SRX2733099" "SRX2733100" "SRX2733101" "SRX2733102" ...
## ..$ SRS_accession : chr [1:333] "SRS2120997" "SRS2120999" "SRS2120998" "SRS2121000" ...
## ..$ SRP_accession : chr [1:333] "SRP103811" "SRP103811" "SRP103811" "SRP103811" ...
## ..$ Sample_name : chr [1:333] "GSM2574469" "GSM2574470" "GSM2574471" "GSM2574472" ...
## ..$ GEO_series : chr [1:333] "GSE97655" "GSE97655" "GSE97655" "GSE97655" ...
## ..$ Library_name : logi [1:333] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:333] "GSM2574469" "GSM2574470" "GSM2574471" "GSM2574472" ...
## ..$ ReleaseDate : chr [1:333] "2017-08-11 16:45:06" "2017-08-11 16:45:06" "2017-08-11 16:45:06" "2017-08-11 16:45:06" ...
## ..$ LoadDate : chr [1:333] "2017-04-14 03:55:52" "2017-04-14 03:55:07" "2017-04-14 03:51:32" "2017-04-14 03:53:05" ...
## ..$ spots : int [1:333] 10609469 11336977 6596750 9550247 7204424 7727320 5692707 7893087 9109440 7000625 ...
## ..$ bases : num [1:333] 2.97e+09 3.17e+09 1.85e+09 2.67e+09 2.02e+09 ...
## ..$ spots_with_mates : int [1:333] 10609469 11336977 6596750 9550247 7204424 7727320 5692707 7893087 9109440 7000625 ...
## ..$ avgLength : int [1:333] 280 280 280 280 280 280 280 280 280 280 ...
## ..$ size_MB : int [1:333] 1215 1291 767 1094 843 900 667 919 1057 806 ...
## ..$ AssemblyName : logi [1:333] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:333] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5443791/SRR5443791.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5443792/SRR5443792.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5443793/SRR5443793.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5443794/SRR5443794.1" ...
## ..$ LibraryName : logi [1:333] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:333] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:333] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:333] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:333] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:333] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:333] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:333] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:333] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:333] "SRP103811" "SRP103811" "SRP103811" "SRP103811" ...
## ..$ BioProject : chr [1:333] "PRJNA382566" "PRJNA382566" "PRJNA382566" "PRJNA382566" ...
## ..$ Study_Pubmed_id : int [1:333] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:333] 382566 382566 382566 382566 382566 382566 382566 382566 382566 382566 ...
## ..$ Sample : chr [1:333] "SRS2120997" "SRS2120999" "SRS2120998" "SRS2121000" ...
## ..$ BioSample : chr [1:333] "SAMN06710485" "SAMN06710484" "SAMN06710483" "SAMN06710406" ...
## ..$ SampleType : chr [1:333] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:333] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:333] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:333] NA NA NA NA NA NA ...
## ..$ source : logi [1:333] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:333] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:333] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:333] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:333] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:333] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:333] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:333] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:333] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:333] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:333] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:333] "SRA553943" "SRA553943" "SRA553943" "SRA553943" ...
## ..$ dbgap_study_accession: logi [1:333] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:333] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:333] "2FB09EFA37416E0AAF0D77DE9468A19F" "2BF852A04E6BB4E2CC8DAA668FFF08AA" "C2851BF8E99D1C4288B2E7CB77724654" "34EF54862234234B1DF7C485D51E4DDB" ...
## ..$ ReadHash : chr [1:333] "981A53A0B5236819E657284936348005" "EE0F4F3FB65114C8739495C0DAABD8CA" "0C94BE90981085FA3E9229E41CC93FDF" "B761A054F876B25D92598D6A115985A5" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 7222 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP106195:human insulin-producing EndoC-βH1 cell line exposed to control (siCTL) versus knockdown (SRpP55):siCTL;SRX2779450,SRX2779451,SRX2779452,SRX2779453,SRX2779454:SRpP55;SRX2779455,SRX2779456,SRX2779457,SRX2779458,SRX2779459;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 200 variables:
## ..$ SRR5499131: int [1:58302] 0 14 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499132: int [1:58302] 0 14 0 2 0 0 0 0 0 0 ...
## ..$ SRR5499133: int [1:58302] 0 20 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499134: int [1:58302] 0 12 0 0 0 0 0 0 0 1 ...
## ..$ SRR5499135: int [1:58302] 0 13 1 0 0 0 1 0 0 0 ...
## ..$ SRR5499136: int [1:58302] 0 8 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499137: int [1:58302] 0 16 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499138: int [1:58302] 0 10 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499139: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499140: int [1:58302] 0 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499141: int [1:58302] 0 10 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499142: int [1:58302] 0 16 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499143: int [1:58302] 0 14 1 1 0 0 0 0 0 0 ...
## ..$ SRR5499144: int [1:58302] 0 10 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499145: int [1:58302] 0 15 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499146: int [1:58302] 0 7 1 1 0 0 0 0 0 0 ...
## ..$ SRR5499147: int [1:58302] 0 10 3 0 0 0 0 0 0 0 ...
## ..$ SRR5499148: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499149: int [1:58302] 0 7 0 1 0 0 0 0 0 0 ...
## ..$ SRR5499150: int [1:58302] 0 17 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499151: int [1:58302] 0 13 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499152: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499153: int [1:58302] 0 8 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499154: int [1:58302] 0 12 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499155: int [1:58302] 0 9 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499156: int [1:58302] 0 10 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499157: int [1:58302] 0 8 3 0 0 0 0 0 0 0 ...
## ..$ SRR5499158: int [1:58302] 0 13 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499159: int [1:58302] 0 16 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499160: int [1:58302] 0 8 3 0 0 0 0 0 0 0 ...
## ..$ SRR5499161: int [1:58302] 1 9 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499162: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499163: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499164: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499165: int [1:58302] 0 11 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499166: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499167: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499168: int [1:58302] 0 9 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499169: int [1:58302] 0 8 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499170: int [1:58302] 0 5 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499171: int [1:58302] 1 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499172: int [1:58302] 0 12 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499173: int [1:58302] 0 5 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499174: int [1:58302] 0 8 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499175: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499176: int [1:58302] 0 5 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499177: int [1:58302] 0 10 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499178: int [1:58302] 1 15 0 0 0 0 0 0 0 1 ...
## ..$ SRR5499179: int [1:58302] 0 9 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499180: int [1:58302] 0 9 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499181: int [1:58302] 1 11 1 1 0 0 0 1 0 0 ...
## ..$ SRR5499182: int [1:58302] 0 9 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499183: int [1:58302] 0 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499184: int [1:58302] 0 12 3 0 0 0 0 0 0 0 ...
## ..$ SRR5499185: int [1:58302] 0 14 4 0 0 0 0 0 0 0 ...
## ..$ SRR5499186: int [1:58302] 0 17 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499187: int [1:58302] 0 15 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499188: int [1:58302] 0 10 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499189: int [1:58302] 0 10 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499190: int [1:58302] 0 16 0 1 0 0 0 0 0 0 ...
## ..$ SRR5499191: int [1:58302] 0 16 0 0 0 0 1 0 0 0 ...
## ..$ SRR5499193: int [1:58302] 0 15 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499194: int [1:58302] 0 15 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499195: int [1:58302] 0 10 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499197: int [1:58302] 0 12 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499198: int [1:58302] 0 11 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499199: int [1:58302] 0 12 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499200: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499202: int [1:58302] 1 11 3 0 0 0 0 0 0 0 ...
## ..$ SRR5499203: int [1:58302] 0 10 2 0 0 0 1 0 0 0 ...
## ..$ SRR5499204: int [1:58302] 0 15 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499205: int [1:58302] 0 15 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499206: int [1:58302] 0 11 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499207: int [1:58302] 0 10 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499208: int [1:58302] 0 17 3 0 0 0 0 0 0 0 ...
## ..$ SRR5499210: int [1:58302] 0 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499211: int [1:58302] 0 21 3 0 0 0 0 0 0 0 ...
## ..$ SRR5499212: int [1:58302] 0 12 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499213: int [1:58302] 0 14 0 1 0 0 0 0 0 0 ...
## ..$ SRR5499214: int [1:58302] 0 9 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499215: int [1:58302] 0 15 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499216: int [1:58302] 0 9 1 0 0 0 1 0 0 0 ...
## ..$ SRR5499217: int [1:58302] 0 22 2 1 0 0 1 0 0 0 ...
## ..$ SRR5499218: int [1:58302] 0 17 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499219: int [1:58302] 0 12 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499220: int [1:58302] 0 16 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499221: int [1:58302] 0 11 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499222: int [1:58302] 0 16 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499223: int [1:58302] 0 15 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499224: int [1:58302] 0 5 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499225: int [1:58302] 0 20 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499226: int [1:58302] 1 13 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499227: int [1:58302] 0 18 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499228: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499229: int [1:58302] 0 12 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499230: int [1:58302] 0 16 2 0 0 0 0 0 0 0 ...
## ..$ SRR5499231: int [1:58302] 0 21 1 0 0 0 0 0 0 0 ...
## ..$ SRR5499232: int [1:58302] 0 10 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499233: int [1:58302] 0 13 1 0 0 0 0 0 0 0 ...
## .. [list output truncated]
## $ TxCounts :'data.frame': 180869 obs. of 200 variables:
## ..$ SRR5499131: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499132: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499133: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499134: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499135: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499136: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499137: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499138: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499139: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499140: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499141: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499142: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499143: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499144: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499145: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499146: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499147: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499148: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499149: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499150: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499151: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499152: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499153: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499154: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499155: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499156: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499157: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499158: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499159: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499160: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499161: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499162: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499163: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499164: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499165: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499166: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499167: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499168: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499169: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499170: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499171: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499172: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499173: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499174: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499175: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499176: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499177: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499178: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499179: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499180: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499181: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499182: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499183: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499184: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499185: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499186: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499187: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499188: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499189: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499190: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499191: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499193: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499194: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499195: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499197: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499198: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499199: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499200: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499202: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499203: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499204: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499205: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499206: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499207: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499208: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499210: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499211: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499212: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499213: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499214: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499215: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499216: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499217: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499218: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499219: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499220: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499221: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499222: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499223: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499224: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499225: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499226: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499227: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499228: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499229: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499230: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499231: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499232: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5499233: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## .. [list output truncated]
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 200 variables:
## ..$ SRR5499131: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499132: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499133: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499134: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499135: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499136: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499137: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499138: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499139: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499140: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499141: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499142: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499143: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499144: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499145: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499146: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499147: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499148: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499149: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499150: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499151: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499152: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499153: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499154: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499155: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499156: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499157: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499158: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499159: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499160: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499161: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499162: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499163: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499164: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499165: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499166: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499167: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499168: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499169: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499170: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499171: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499172: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499173: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499174: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499175: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499176: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499177: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499178: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499179: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499180: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499181: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499182: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499183: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499184: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499185: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499186: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499187: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499188: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499189: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499190: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499191: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499193: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499194: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499195: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499197: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499198: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499199: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499200: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499202: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499203: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499204: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499205: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499206: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499207: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499208: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499210: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499211: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499212: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499213: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499214: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499215: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499216: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499217: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499218: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499219: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499220: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499221: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499222: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499223: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499224: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499225: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499226: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499227: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499228: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499229: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499230: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499231: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499232: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5499233: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## .. [list output truncated]
## $ MetadataSummary:'data.frame': 200 obs. of 7 variables:
## ..$ QC_summary : chr [1:200] "WARN(1,5,7,8)" "WARN(1,5,7,8)" "WARN(1,5,7,8)" "WARN(1,5,7,8)" ...
## ..$ SRX_accession: chr [1:200] "SRX2779450" "SRX2779450" "SRX2779450" "SRX2779450" ...
## ..$ SRS_accession: chr [1:200] "SRS2162699" "SRS2162699" "SRS2162699" "SRS2162699" ...
## ..$ SRP_accession: chr [1:200] "SRP106195" "SRP106195" "SRP106195" "SRP106195" ...
## ..$ Sample_name : chr [1:200] "GSM2597305" "GSM2597305" "GSM2597305" "GSM2597305" ...
## ..$ GEO_series : chr [1:200] "GSE98485" "GSE98485" "GSE98485" "GSE98485" ...
## ..$ Library_name : logi [1:200] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 200 obs. of 52 variables:
## ..$ QC_summary : chr [1:200] "WARN(1,5,7,8)" "WARN(1,5,7,8)" "WARN(1,5,7,8)" "WARN(1,5,7,8)" ...
## ..$ SRX_accession : chr [1:200] "SRX2779450" "SRX2779450" "SRX2779450" "SRX2779450" ...
## ..$ SRS_accession : chr [1:200] "SRS2162699" "SRS2162699" "SRS2162699" "SRS2162699" ...
## ..$ SRP_accession : chr [1:200] "SRP106195" "SRP106195" "SRP106195" "SRP106195" ...
## ..$ Sample_name : chr [1:200] "GSM2597305" "GSM2597305" "GSM2597305" "GSM2597305" ...
## ..$ GEO_series : chr [1:200] "GSE98485" "GSE98485" "GSE98485" "GSE98485" ...
## ..$ Library_name : logi [1:200] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:200] "GSM2597305" "GSM2597305" "GSM2597305" "GSM2597305" ...
## ..$ ReleaseDate : chr [1:200] "2018-02-05 09:02:09" "2018-02-05 09:02:09" "2018-02-05 09:02:09" "2018-02-05 09:02:09" ...
## ..$ LoadDate : chr [1:200] "2017-05-02 18:15:39" "2017-05-02 18:15:44" "2017-05-02 18:15:32" "2017-05-02 18:18:23" ...
## ..$ spots : int [1:200] 4000000 4000000 4000000 4000000 4000000 4000000 4000000 4000000 438318 4000000 ...
## ..$ bases : int [1:200] 808000000 808000000 808000000 808000000 808000000 808000000 808000000 808000000 88540236 808000000 ...
## ..$ spots_with_mates : int [1:200] 4000000 4000000 4000000 4000000 4000000 4000000 4000000 4000000 438318 4000000 ...
## ..$ avgLength : int [1:200] 202 202 202 202 202 202 202 202 202 202 ...
## ..$ size_MB : int [1:200] 534 540 558 534 548 552 539 562 64 549 ...
## ..$ AssemblyName : logi [1:200] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:200] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5499131/SRR5499131.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5499132/SRR5499132.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5499133/SRR5499133.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5499134/SRR5499134.1" ...
## ..$ LibraryName : logi [1:200] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:200] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:200] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:200] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:200] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:200] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:200] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:200] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:200] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:200] "SRP106195" "SRP106195" "SRP106195" "SRP106195" ...
## ..$ BioProject : chr [1:200] "PRJNA385196" "PRJNA385196" "PRJNA385196" "PRJNA385196" ...
## ..$ Study_Pubmed_id : int [1:200] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:200] 385196 385196 385196 385196 385196 385196 385196 385196 385196 385196 ...
## ..$ Sample : chr [1:200] "SRS2162699" "SRS2162699" "SRS2162699" "SRS2162699" ...
## ..$ BioSample : chr [1:200] "SAMN06883725" "SAMN06883725" "SAMN06883725" "SAMN06883725" ...
## ..$ SampleType : chr [1:200] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:200] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:200] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:200] NA NA NA NA NA NA ...
## ..$ source : logi [1:200] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:200] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:200] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:200] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:200] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:200] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:200] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:200] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:200] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:200] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:200] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:200] "SRA558862" "SRA558862" "SRA558862" "SRA558862" ...
## ..$ dbgap_study_accession: logi [1:200] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:200] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:200] "2A838B296B83AC7695AAF62CD063FF2F" "1AB7620A86CCBEC9C374F3ECEFBF0656" "8AEE8445BF5355143EDEA711F8FADA99" "460D8D411EBDC0E38CAA56B5672987F3" ...
## ..$ ReadHash : chr [1:200] "20D4BACA0737C2D44494D009F181FC6A" "E755AED5526F20479B0DD7EBF85932C8" "5A98AC485185935B48D2139468006613" "53530AB9B579CF58894F43E3EBF82C97" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP121445:non-diabetic control versus type 1 diabetes (T1D):control;SRX3325355,SRX3325356,SRX3325357, SRX3325358,SRX3325359:T1D;SRX3325360,SRX3325361,SRX3325362;age,sex## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR6216690: int [1:58302] 0 4 4 0 0 0 0 0 0 2 ...
## ..$ SRR6216691: int [1:58302] 0 5 0 1 0 0 0 1 0 0 ...
## ..$ SRR6216692: int [1:58302] 0 3 0 0 0 0 0 2 0 3 ...
## ..$ SRR6216693: int [1:58302] 0 1 0 0 0 0 0 0 0 5 ...
## ..$ SRR6216694: int [1:58302] 2 9 0 0 0 0 0 1 0 0 ...
## ..$ SRR6216695: int [1:58302] 0 3 0 0 0 0 0 0 0 1 ...
## ..$ SRR6216696: int [1:58302] 0 12 0 3 0 0 0 0 0 0 ...
## ..$ SRR6216697: int [1:58302] 0 12 2 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR6216690: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6216691: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6216692: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6216693: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6216694: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6216695: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6216696: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6216697: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR6216690: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR6216691: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR6216692: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR6216693: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR6216694: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR6216695: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR6216696: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR6216697: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "WARN(2,6)" "WARN(4,6)" "FAIL(6)" "FAIL(2)" ...
## ..$ SRX_accession: chr [1:8] "SRX3325355" "SRX3325356" "SRX3325357" "SRX3325358" ...
## ..$ SRS_accession: chr [1:8] "SRS2629799" "SRS2629800" "SRS2629801" "SRS2629802" ...
## ..$ SRP_accession: chr [1:8] "SRP121445" "SRP121445" "SRP121445" "SRP121445" ...
## ..$ Sample_name : chr [1:8] "GSM2830482" "GSM2830483" "GSM2830484" "GSM2830485" ...
## ..$ GEO_series : chr [1:8] "GSE106148" "GSE106148" "GSE106148" "GSE106148" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "WARN(2,6)" "WARN(4,6)" "FAIL(6)" "FAIL(2)" ...
## ..$ SRX_accession : chr [1:8] "SRX3325355" "SRX3325356" "SRX3325357" "SRX3325358" ...
## ..$ SRS_accession : chr [1:8] "SRS2629799" "SRS2629800" "SRS2629801" "SRS2629802" ...
## ..$ SRP_accession : chr [1:8] "SRP121445" "SRP121445" "SRP121445" "SRP121445" ...
## ..$ Sample_name : chr [1:8] "GSM2830482" "GSM2830483" "GSM2830484" "GSM2830485" ...
## ..$ GEO_series : chr [1:8] "GSE106148" "GSE106148" "GSE106148" "GSE106148" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM2830482" "GSM2830483" "GSM2830484" "GSM2830485" ...
## ..$ ReleaseDate : chr [1:8] "2017-12-15 12:57:14" "2017-12-15 12:57:14" "2017-12-15 12:57:14" "2017-12-15 12:57:14" ...
## ..$ LoadDate : chr [1:8] "2017-10-25 17:23:04" "2017-10-25 17:37:43" "2017-10-25 17:31:38" "2017-10-25 17:20:04" ...
## ..$ spots : int [1:8] 29348779 54298212 49700063 28482516 60466668 50199063 51130384 108061188
## ..$ bases : num [1:8] 2.93e+09 5.43e+09 4.97e+09 2.85e+09 6.05e+09 ...
## ..$ spots_with_mates : int [1:8] 29348779 54298212 49700063 28482516 60466668 50199063 51130384 108061188
## ..$ avgLength : int [1:8] 100 100 100 100 100 100 100 100
## ..$ size_MB : int [1:8] 987 1784 1648 927 2017 1656 1704 3887
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6216690/SRR6216690.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6216691/SRR6216691.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6216692/SRR6216692.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6216693/SRR6216693.1" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:8] "SRP121445" "SRP121445" "SRP121445" "SRP121445" ...
## ..$ BioProject : chr [1:8] "PRJNA415746" "PRJNA415746" "PRJNA415746" "PRJNA415746" ...
## ..$ Study_Pubmed_id : int [1:8] 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:8] 415746 415746 415746 415746 415746 415746 415746 415746
## ..$ Sample : chr [1:8] "SRS2629799" "SRS2629800" "SRS2629801" "SRS2629802" ...
## ..$ BioSample : chr [1:8] "SAMN07834003" "SAMN07834010" "SAMN07834009" "SAMN07834008" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA624586" "SRA624586" "SRA624586" "SRA624586" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "026C8DF94E81A22CF37B7C673C25F59E" "60AF4165C39B012C632D9A8292AE6095" "F1B28FEA8D9F68CED3FE9B49376748C9" "27915190EA5EF82B51762509EB10A0B4" ...
## ..$ ReadHash : chr [1:8] "B83BD20C092F5560EFC08BDD2BB0781F" "2C39D4B026188992CC8AF298A96D307C" "8010952DF6CA0546191B57E7FD1EED4A" "5C670707EFD3D9B224384F9BA17FFC41" ...
## $ absent : chr(0)## SRP127362:control vs cytokine treatment:control;SRX3503795,SRX3503797,SRX3503799,SRX3503801,SRX3503803:cytokine treatment; SRX3503796,SRX3503798,SRX3503800,SRX35038002,SRX3503804;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 7 variables:
## ..$ SRR6410768: int [1:58302] 0 72 14 0 0 0 0 0 0 2 ...
## ..$ SRR6410770: int [1:58302] 1 47 6 1 0 0 0 0 0 0 ...
## ..$ SRR6410771: int [1:58302] 0 47 7 0 0 0 0 0 0 1 ...
## ..$ SRR6410772: int [1:58302] 0 83 14 0 0 0 0 0 0 0 ...
## ..$ SRR6410773: int [1:58302] 0 61 12 0 0 0 0 0 0 1 ...
## ..$ SRR6410774: int [1:58302] 0 84 14 0 0 0 0 0 0 2 ...
## ..$ SRR6410776: int [1:58302] 1 208 33 0 0 0 0 0 0 3 ...
## $ TxCounts :'data.frame': 180869 obs. of 7 variables:
## ..$ SRR6410768: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6410770: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6410771: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6410772: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6410773: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6410774: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6410776: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 7 variables:
## ..$ SRR6410768: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR6410770: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR6410771: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR6410772: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR6410773: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR6410774: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR6410776: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 7 obs. of 7 variables:
## ..$ QC_summary : chr [1:7] "PASS" "PASS" "WARN(8)" "PASS" ...
## ..$ SRX_accession: chr [1:7] "SRX3503795" "SRX3503797" "SRX3503798" "SRX3503799" ...
## ..$ SRS_accession: chr [1:7] "SRS2781417" "SRS2781419" "SRS2781420" "SRS2781421" ...
## ..$ SRP_accession: chr [1:7] "SRP127362" "SRP127362" "SRP127362" "SRP127362" ...
## ..$ Sample_name : chr [1:7] "GSM2897819" "GSM2897821" "GSM2897822" "GSM2897823" ...
## ..$ GEO_series : chr [1:7] "GSE108413" "GSE108413" "GSE108413" "GSE108413" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 7 obs. of 52 variables:
## ..$ QC_summary : chr [1:7] "PASS" "PASS" "WARN(8)" "PASS" ...
## ..$ SRX_accession : chr [1:7] "SRX3503795" "SRX3503797" "SRX3503798" "SRX3503799" ...
## ..$ SRS_accession : chr [1:7] "SRS2781417" "SRS2781419" "SRS2781420" "SRS2781421" ...
## ..$ SRP_accession : chr [1:7] "SRP127362" "SRP127362" "SRP127362" "SRP127362" ...
## ..$ Sample_name : chr [1:7] "GSM2897819" "GSM2897821" "GSM2897822" "GSM2897823" ...
## ..$ GEO_series : chr [1:7] "GSE108413" "GSE108413" "GSE108413" "GSE108413" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:7] "GSM2897819" "GSM2897821" "GSM2897822" "GSM2897823" ...
## ..$ ReleaseDate : chr [1:7] "2018-08-03 07:14:10" "2018-08-03 07:14:10" "2018-08-03 07:14:10" "2018-08-03 07:14:10" ...
## ..$ LoadDate : chr [1:7] "2017-12-21 16:49:29" "2017-12-21 17:14:30" "2017-12-21 19:01:04" "2017-12-21 16:46:01" ...
## ..$ spots : int [1:7] 85796850 106684944 88982796 85596458 90105556 92060512 101365268
## ..$ bases : num [1:7] 1.73e+10 2.16e+10 1.80e+10 1.73e+10 1.82e+10 ...
## ..$ spots_with_mates : int [1:7] 85796850 106684944 88982796 85596458 90105556 92060512 101365268
## ..$ avgLength : int [1:7] 202 202 202 202 202 202 202
## ..$ size_MB : int [1:7] 11912 14627 12249 11862 12452 12868 13605
## ..$ AssemblyName : logi [1:7] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:7] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6410768/SRR6410768.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6410770/SRR6410770.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6410771/SRR6410771.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6410772/SRR6410772.1" ...
## ..$ LibraryName : logi [1:7] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:7] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:7] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:7] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:7] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:7] 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:7] 0 0 0 0 0 0 0
## ..$ Platform : chr [1:7] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:7] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:7] "SRP127362" "SRP127362" "SRP127362" "SRP127362" ...
## ..$ BioProject : chr [1:7] "PRJNA427190" "PRJNA427190" "PRJNA427190" "PRJNA427190" ...
## ..$ Study_Pubmed_id : int [1:7] 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:7] 427190 427190 427190 427190 427190 427190 427190
## ..$ Sample : chr [1:7] "SRS2781417" "SRS2781419" "SRS2781420" "SRS2781421" ...
## ..$ BioSample : chr [1:7] "SAMN08225441" "SAMN08225449" "SAMN08225448" "SAMN08225447" ...
## ..$ SampleType : chr [1:7] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:7] 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:7] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:7] NA NA NA NA NA NA ...
## ..$ source : logi [1:7] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:7] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:7] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:7] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:7] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:7] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:7] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:7] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:7] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:7] "SRA641102" "SRA641102" "SRA641102" "SRA641102" ...
## ..$ dbgap_study_accession: logi [1:7] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:7] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:7] "2305E6A8AF47BCE8A009C236D0F4CFFC" "BD231B6E97A718B17CFB19D695E6E61F" "A4B81A733DAAF933437486A38A569957" "F4D054647ABC6BBBEB581F7B079DF6A8" ...
## ..$ ReadHash : chr [1:7] "30EB9D96973140E75260A1BBE33B0DF8" "168D792BF036B875ABE363CF863683F3" "ED56892EBDBAF08305A7781BEE1188B7" "E0B2F896E3C6E438E54E890C6D810C75" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP128998:high glucose versus high glucose VPA (valproic acid):high glucose;SRX3557428,SRX3557429, SRX3557430:high glucose VPA;SRX3557431,SRX3557432,SRX3557433;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR6467479: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467480: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467481: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467482: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467483: int [1:58302] 0 0 1 0 0 0 2 0 2 0 ...
## ..$ SRR6467484: int [1:58302] 1 0 0 1 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR6467479: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467480: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467481: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467482: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467483: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467484: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR6467479: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## ..$ SRR6467480: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## ..$ SRR6467481: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## ..$ SRR6467482: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## ..$ SRR6467483: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## ..$ SRR6467484: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX3557428" "SRX3557429" "SRX3557430" "SRX3557431" ...
## ..$ SRS_accession: chr [1:6] "SRS2830728" "SRS2830730" "SRS2830729" "SRS2830731" ...
## ..$ SRP_accession: chr [1:6] "SRP128998" "SRP128998" "SRP128998" "SRP128998" ...
## ..$ Sample_name : chr [1:6] "GSM2932791" "GSM2932792" "GSM2932793" "GSM2932794" ...
## ..$ GEO_series : chr [1:6] "GSE109140" "GSE109140" "GSE109140" "GSE109140" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX3557428" "SRX3557429" "SRX3557430" "SRX3557431" ...
## ..$ SRS_accession : chr [1:6] "SRS2830728" "SRS2830730" "SRS2830729" "SRS2830731" ...
## ..$ SRP_accession : chr [1:6] "SRP128998" "SRP128998" "SRP128998" "SRP128998" ...
## ..$ Sample_name : chr [1:6] "GSM2932791" "GSM2932792" "GSM2932793" "GSM2932794" ...
## ..$ GEO_series : chr [1:6] "GSE109140" "GSE109140" "GSE109140" "GSE109140" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2932791" "GSM2932792" "GSM2932793" "GSM2932794" ...
## ..$ ReleaseDate : chr [1:6] "2018-01-23 15:04:10" "2018-01-23 15:04:10" "2018-01-23 15:04:10" "2018-01-23 15:04:10" ...
## ..$ LoadDate : chr [1:6] "2018-01-12 10:01:15" "2018-01-12 10:04:17" "2018-01-12 10:10:14" "2018-01-12 10:06:06" ...
## ..$ spots : int [1:6] 44859175 46794649 51306435 41954691 60925401 42398824
## ..$ bases : num [1:6] 2.69e+09 2.81e+09 3.08e+09 2.52e+09 3.66e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 60 60 60 60 60 60
## ..$ size_MB : int [1:6] 914 952 1043 854 1250 863
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR6467479/SRR6467479.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6467480/SRR6467480.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR6467481/SRR6467481.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6467482/SRR6467482.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP128998" "SRP128998" "SRP128998" "SRP128998" ...
## ..$ BioProject : chr [1:6] "PRJNA429757" "PRJNA429757" "PRJNA429757" "PRJNA429757" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 429757 429757 429757 429757 429757 429757
## ..$ Sample : chr [1:6] "SRS2830728" "SRS2830730" "SRS2830729" "SRS2830731" ...
## ..$ BioSample : chr [1:6] "SAMN08358849" "SAMN08358862" "SAMN08358861" "SAMN08358860" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA646226" "SRA646226" "SRA646226" "SRA646226" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "ADEBB1C6DD68CFDF0A8510903AF52B5A" "5B09D2F1CDFB8F46313AB88C47DC6D71" "14516F891FFBD7F5314DBF8F6E018D2E" "894DF0BD9BE18A5F880DD1CB6CCE4D2D" ...
## ..$ ReadHash : chr [1:6] "47C8C595ADA9ECE53D1B111A501C8E9F" "1DD6759600718B55ED00600128F9BB7C" "3B3E0F2EA39070668C0A76388AF5D78E" "DFDDF251687AD7ECB5E5FFD7B75CC281" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP128998:low glucose versus low glucose VPA (valproic acid):low glucose;SRX3557434,SRX3557435,SRX3557436: low glucose VPA;SRX3557437,SRX3557438,SRX3557439;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR6467485: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467486: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467487: int [1:58302] 0 2 0 1 0 0 0 0 0 1 ...
## ..$ SRR6467488: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467489: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467490: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR6467485: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467486: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467487: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467488: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467489: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6467490: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR6467485: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## ..$ SRR6467486: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## ..$ SRR6467487: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## ..$ SRR6467488: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## ..$ SRR6467489: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## ..$ SRR6467490: chr [1:30] "SE" "Sanger/Illumina1.9" "60" "60" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX3557434" "SRX3557435" "SRX3557436" "SRX3557437" ...
## ..$ SRS_accession: chr [1:6] "SRS2830733" "SRS2830734" "SRS2830735" "SRS2830736" ...
## ..$ SRP_accession: chr [1:6] "SRP128998" "SRP128998" "SRP128998" "SRP128998" ...
## ..$ Sample_name : chr [1:6] "GSM2932797" "GSM2932798" "GSM2932799" "GSM2932800" ...
## ..$ GEO_series : chr [1:6] "GSE109140" "GSE109140" "GSE109140" "GSE109140" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX3557434" "SRX3557435" "SRX3557436" "SRX3557437" ...
## ..$ SRS_accession : chr [1:6] "SRS2830733" "SRS2830734" "SRS2830735" "SRS2830736" ...
## ..$ SRP_accession : chr [1:6] "SRP128998" "SRP128998" "SRP128998" "SRP128998" ...
## ..$ Sample_name : chr [1:6] "GSM2932797" "GSM2932798" "GSM2932799" "GSM2932800" ...
## ..$ GEO_series : chr [1:6] "GSE109140" "GSE109140" "GSE109140" "GSE109140" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2932797" "GSM2932798" "GSM2932799" "GSM2932800" ...
## ..$ ReleaseDate : chr [1:6] "2018-01-23 15:04:10" "2018-01-23 15:04:10" "2018-01-23 15:04:10" "2018-01-23 15:04:10" ...
## ..$ LoadDate : chr [1:6] "2018-01-12 10:02:55" "2018-01-12 10:09:54" "2018-01-12 10:04:55" "2018-01-12 10:05:35" ...
## ..$ spots : int [1:6] 41074338 63603971 56422849 45615658 44499956 51232926
## ..$ bases : num [1:6] 2.46e+09 3.82e+09 3.39e+09 2.74e+09 2.67e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 60 60 60 60 60 60
## ..$ size_MB : int [1:6] 838 1295 1155 928 906 1046
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6467485/SRR6467485.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR6467486/SRR6467486.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR6467487/SRR6467487.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6467488/SRR6467488.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP128998" "SRP128998" "SRP128998" "SRP128998" ...
## ..$ BioProject : chr [1:6] "PRJNA429757" "PRJNA429757" "PRJNA429757" "PRJNA429757" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 429757 429757 429757 429757 429757 429757
## ..$ Sample : chr [1:6] "SRS2830733" "SRS2830734" "SRS2830735" "SRS2830736" ...
## ..$ BioSample : chr [1:6] "SAMN08358857" "SAMN08358856" "SAMN08358855" "SAMN08358854" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA646226" "SRA646226" "SRA646226" "SRA646226" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "36973298B3FC05DE2042D809339B5BFC" "D2B58F3D80082146573C567363E063A1" "33F081B0429BC828C5E7B41CB68C6F6E" "FAD86B2A0F160567EA4415056EC10D77" ...
## ..$ ReadHash : chr [1:6] "456570FB7A8CC4D13E58D5397ABC99E3" "1CE3568BB59BC601391895A0BE4615FE" "E2955866DAA1D1000CDDC5CEC22057B7" "8877235FD1791D10C7522A72D550D3BD" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP135788:CD3+ T cells of nondiabetic individuals vs type 1 diabetes:nondiabetic;SRX3797556SRX3797557,SRX3797558,SRX3797559,SRX3797560,SRX3797561,SRX3797562,SRX3797563,SRX3797564,SRX3797565,SRX3797566,SRX3797567,SRX3797568,SRX3797569,SRX3797570,SRX3797571,SRX3797572,SRX3797573,:type 1 diabetes;SRX3797574,SRX3797575,SRX3797576,SRX3797577,SRX3797578,SRX3797579,SRX3797580,SRX3797581,SRX3797582,SRX3797583,SRX3797584,SRX3797585,SRX3797585,SRX3797586,SRX3797587,SRX3797588,SRX3797589,SRX3797590,SRX3797591,SRX3797592,SRX3797593,SRX3797594,SRX3797595,SRX3797596,SRX3797597,SRX3797598,SRX3797599,SRX3797600,SRX3797601,SRX3797602,SRX3797603,SRX3797604;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 40 variables:
## ..$ SRR6841731: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841732: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841733: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841734: int [1:58302] 0 0 0 0 0 0 0 1 1 1 ...
## ..$ SRR6841735: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR6841736: int [1:58302] 0 0 0 0 0 0 0 1 0 0 ...
## ..$ SRR6841738: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841739: int [1:58302] 0 0 0 0 0 0 0 0 1 0 ...
## ..$ SRR6841740: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841741: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841742: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841743: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841745: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841746: int [1:58302] 1 0 0 0 0 0 0 1 0 0 ...
## ..$ SRR6841747: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841748: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841749: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841750: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841751: int [1:58302] 0 0 0 0 0 0 0 1 0 2 ...
## ..$ SRR6841753: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841754: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841755: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841757: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR6841758: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR6841759: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841761: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841762: int [1:58302] 0 0 0 0 0 0 0 0 1 0 ...
## ..$ SRR6841763: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841764: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841765: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841766: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841767: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841768: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841770: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841771: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841772: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841773: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841774: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841775: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841776: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 40 variables:
## ..$ SRR6841731: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841732: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841733: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841734: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841735: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841736: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841738: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841739: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841740: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841741: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841742: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841743: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841745: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841746: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841747: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841748: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841749: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841750: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841751: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841753: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841754: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841755: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841757: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841758: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841759: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841761: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841762: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841763: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841764: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841765: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841766: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841767: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841768: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841770: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841771: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841772: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841773: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841774: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841775: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6841776: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 40 variables:
## ..$ SRR6841731: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841732: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841733: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841734: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841735: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841736: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841738: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841739: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841740: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841741: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841742: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841743: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841745: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841746: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841747: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841748: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841749: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841750: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841751: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841753: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841754: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841755: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841757: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841758: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841759: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841761: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841762: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841763: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841764: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841765: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841766: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841767: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841768: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841770: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841771: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841772: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841773: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841774: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841775: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6841776: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 40 obs. of 7 variables:
## ..$ QC_summary : chr [1:40] "FAIL(4,5,6)" "FAIL(4,6)" "FAIL(4,5,6,7)" "FAIL(4,5,6)" ...
## ..$ SRX_accession: chr [1:40] "SRX3797558" "SRX3797559" "SRX3797560" "SRX3797561" ...
## ..$ SRS_accession: chr [1:40] "SRS3049637" "SRS3049639" "SRS3049638" "SRS3049640" ...
## ..$ SRP_accession: chr [1:40] "SRP135788" "SRP135788" "SRP135788" "SRP135788" ...
## ..$ Sample_name : chr [1:40] "GSM3043167" "GSM3043168" "GSM3043169" "GSM3043170" ...
## ..$ GEO_series : chr [1:40] "GSE111876" "GSE111876" "GSE111876" "GSE111876" ...
## ..$ Library_name : logi [1:40] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 40 obs. of 52 variables:
## ..$ QC_summary : chr [1:40] "FAIL(4,5,6)" "FAIL(4,6)" "FAIL(4,5,6,7)" "FAIL(4,5,6)" ...
## ..$ SRX_accession : chr [1:40] "SRX3797558" "SRX3797559" "SRX3797560" "SRX3797561" ...
## ..$ SRS_accession : chr [1:40] "SRS3049637" "SRS3049639" "SRS3049638" "SRS3049640" ...
## ..$ SRP_accession : chr [1:40] "SRP135788" "SRP135788" "SRP135788" "SRP135788" ...
## ..$ Sample_name : chr [1:40] "GSM3043167" "GSM3043168" "GSM3043169" "GSM3043170" ...
## ..$ GEO_series : chr [1:40] "GSE111876" "GSE111876" "GSE111876" "GSE111876" ...
## ..$ Library_name : logi [1:40] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:40] "GSM3043167" "GSM3043168" "GSM3043169" "GSM3043170" ...
## ..$ ReleaseDate : chr [1:40] "2018-03-30 17:33:06" "2018-03-30 17:33:06" "2018-03-30 17:33:06" "2018-03-30 17:33:07" ...
## ..$ LoadDate : chr [1:40] "2018-03-15 13:52:15" "2018-03-15 13:52:40" "2018-03-15 13:51:59" "2018-03-15 13:52:56" ...
## ..$ spots : int [1:40] 3056002 4283582 2197334 3636308 6007724 3899715 7127332 5317592 4320885 11045528 ...
## ..$ bases : int [1:40] 155856102 218462682 112064034 185451708 306393924 198885465 363493932 271197192 220365135 563321928 ...
## ..$ spots_with_mates : int [1:40] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:40] 51 51 51 51 51 51 51 51 51 51 ...
## ..$ size_MB : int [1:40] 52 72 37 61 102 66 121 90 73 187 ...
## ..$ AssemblyName : logi [1:40] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:40] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6841731/SRR6841731.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6841732/SRR6841732.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6841733/SRR6841733.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR6841734/SRR6841734.1" ...
## ..$ LibraryName : logi [1:40] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:40] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:40] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:40] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:40] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:40] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:40] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:40] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:40] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:40] "SRP135788" "SRP135788" "SRP135788" "SRP135788" ...
## ..$ BioProject : chr [1:40] "PRJNA438490" "PRJNA438490" "PRJNA438490" "PRJNA438490" ...
## ..$ Study_Pubmed_id : int [1:40] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:40] 438490 438490 438490 438490 438490 438490 438490 438490 438490 438490 ...
## ..$ Sample : chr [1:40] "SRS3049637" "SRS3049639" "SRS3049638" "SRS3049640" ...
## ..$ BioSample : chr [1:40] "SAMN08718025" "SAMN08718024" "SAMN08718023" "SAMN08718022" ...
## ..$ SampleType : chr [1:40] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:40] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:40] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:40] NA NA NA NA NA NA ...
## ..$ source : logi [1:40] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:40] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:40] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:40] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:40] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:40] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:40] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:40] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:40] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:40] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:40] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:40] "SRA666810" "SRA666810" "SRA666810" "SRA666810" ...
## ..$ dbgap_study_accession: logi [1:40] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:40] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:40] "96E157FD61076AC766B61BBC238EFB7D" "0F6FF1EB7AA3F69A8F86924C8F1C9248" "B8610C83A43F0AD113F188BCD1B15608" "AD3BDFD3BCF7B3CEDD38FA0D27F78E31" ...
## ..$ ReadHash : chr [1:40] "850EE0802CF317D27325A40D3E0D594C" "19A9A7A33755953D7AC4872476B2A50E" "471A84201D48E5BE44BEEA95F5BE6720" "B5A62D265457020C9FBD21056A28502F" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 104 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP151530:BCL11A control vs BCL11A knockdown:control;SRX4317511,SRX4317512,SRX4317513,SRX4317514: knockdown;SRX4317515,SRX4317516,SRX4317517,SRX4317518;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR7446963: int [1:58302] 1 16 4 0 0 0 0 0 0 0 ...
## ..$ SRR7446964: int [1:58302] 0 11 0 0 0 0 0 0 0 0 ...
## ..$ SRR7446966: int [1:58302] 0 19 1 0 0 0 0 0 0 0 ...
## ..$ SRR7446967: int [1:58302] 0 9 3 0 0 0 0 0 0 0 ...
## ..$ SRR7446968: int [1:58302] 0 14 5 0 0 0 0 0 0 1 ...
## ..$ SRR7446969: int [1:58302] 0 73 3 0 0 0 0 1 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR7446963: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7446964: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7446966: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7446967: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7446968: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7446969: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR7446963: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "109" ...
## ..$ SRR7446964: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "100" ...
## ..$ SRR7446966: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "106" ...
## ..$ SRR7446967: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "109" ...
## ..$ SRR7446968: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "101" ...
## ..$ SRR7446969: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "101" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(4,8)" "WARN(8)" "WARN(4,8)" "WARN(4,8)" ...
## ..$ SRX_accession: chr [1:6] "SRX4317512" "SRX4317513" "SRX4317515" "SRX4317516" ...
## ..$ SRS_accession: chr [1:6] "SRS3480514" "SRS3480515" "SRS3480517" "SRS3480518" ...
## ..$ SRP_accession: chr [1:6] "SRP151530" "SRP151530" "SRP151530" "SRP151530" ...
## ..$ Sample_name : chr [1:6] "GSM3230058" "GSM3230059" "GSM3230061" "GSM3230062" ...
## ..$ GEO_series : chr [1:6] "GSE116369" "GSE116369" "GSE116369" "GSE116369" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(4,8)" "WARN(8)" "WARN(4,8)" "WARN(4,8)" ...
## ..$ SRX_accession : chr [1:6] "SRX4317512" "SRX4317513" "SRX4317515" "SRX4317516" ...
## ..$ SRS_accession : chr [1:6] "SRS3480514" "SRS3480515" "SRS3480517" "SRS3480518" ...
## ..$ SRP_accession : chr [1:6] "SRP151530" "SRP151530" "SRP151530" "SRP151530" ...
## ..$ Sample_name : chr [1:6] "GSM3230058" "GSM3230059" "GSM3230061" "GSM3230062" ...
## ..$ GEO_series : chr [1:6] "GSE116369" "GSE116369" "GSE116369" "GSE116369" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM3230058" "GSM3230059" "GSM3230061" "GSM3230062" ...
## ..$ ReleaseDate : chr [1:6] "2018-07-02 10:15:09" "2018-07-02 10:15:09" "2018-07-02 10:15:09" "2018-07-02 10:15:09" ...
## ..$ LoadDate : chr [1:6] "2018-06-28 08:34:09" "2018-06-28 08:52:30" "2018-06-28 08:31:27" "2018-06-28 08:20:45" ...
## ..$ spots : int [1:6] 82332191 96725793 83878684 58532084 80773903 74225423
## ..$ bases : num [1:6] 1.78e+10 1.80e+10 1.79e+10 1.26e+10 1.50e+10 ...
## ..$ spots_with_mates : int [1:6] 82332191 96725793 83878684 58532084 80773903 74225423
## ..$ avgLength : int [1:6] 216 186 213 215 185 188
## ..$ size_MB : int [1:6] 7550 7463 7646 5364 6271 5890
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7446963/SRR7446963.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7446964/SRR7446964.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7446966/SRR7446966.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7446967/SRR7446967.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:6] "SRP151530" "SRP151530" "SRP151530" "SRP151530" ...
## ..$ BioProject : chr [1:6] "PRJNA478311" "PRJNA478311" "PRJNA478311" "PRJNA478311" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 478311 478311 478311 478311 478311 478311
## ..$ Sample : chr [1:6] "SRS3480514" "SRS3480515" "SRS3480517" "SRS3480518" ...
## ..$ BioSample : chr [1:6] "SAMN09510301" "SAMN09510300" "SAMN09510298" "SAMN09510297" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA730101" "SRA730101" "SRA730101" "SRA730101" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "2564E2D33CADF64A73450F7825F40456" "D65950B882CB5AB4C7B07B28A9BCB836" "A95373880C8783407AF3BDC91FC8ABE9" "213AB2DACE512E96B756058C54EA18FD" ...
## ..$ ReadHash : chr [1:6] "796408CD850E80B0EEC96B9EF90FDC5F" "0B2849A58217EBA13968A8F18D1B8D13" "7D8E3C9875CD76C9D95F3E6847330410" "0BB0F340466751D558495B682148649B" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP107327:control IL6Ra- versus IL6Ra+ in obese PBMC:IL6Ra-;SRX2833985,SRX2833986,SRX2833988:IL6Ra+;SRX2833984,SRX2833987,SRX2833989;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR5575722: int [1:58302] 0 22 19 0 0 0 0 0 0 1 ...
## ..$ SRR5575723: int [1:58302] 3 81 30 0 0 0 0 0 0 0 ...
## ..$ SRR5575724: int [1:58302] 1 75 28 0 0 0 0 0 0 0 ...
## ..$ SRR5575725: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575726: int [1:58302] 1 116 26 0 0 0 0 0 0 2 ...
## ..$ SRR5575727: int [1:58302] 0 65 9 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR5575722: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575723: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575724: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575725: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575726: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575727: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR5575722: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575723: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575724: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575725: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575726: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575727: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(3,4,6)" "PASS" "PASS" "FAIL(3,4)" ...
## ..$ SRX_accession: chr [1:6] "SRX2833984" "SRX2833985" "SRX2833986" "SRX2833987" ...
## ..$ SRS_accession: chr [1:6] "SRS2208367" "SRS2208368" "SRS2208371" "SRS2208369" ...
## ..$ SRP_accession: chr [1:6] "SRP107327" "SRP107327" "SRP107327" "SRP107327" ...
## ..$ Sample_name : chr [1:6] "GSM2631758" "GSM2631759" "GSM2631760" "GSM2631761" ...
## ..$ GEO_series : chr [1:6] "GSE99068" "GSE99068" "GSE99068" "GSE99068" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(3,4,6)" "PASS" "PASS" "FAIL(3,4)" ...
## ..$ SRX_accession : chr [1:6] "SRX2833984" "SRX2833985" "SRX2833986" "SRX2833987" ...
## ..$ SRS_accession : chr [1:6] "SRS2208367" "SRS2208368" "SRS2208371" "SRS2208369" ...
## ..$ SRP_accession : chr [1:6] "SRP107327" "SRP107327" "SRP107327" "SRP107327" ...
## ..$ Sample_name : chr [1:6] "GSM2631758" "GSM2631759" "GSM2631760" "GSM2631761" ...
## ..$ GEO_series : chr [1:6] "GSE99068" "GSE99068" "GSE99068" "GSE99068" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2631758" "GSM2631759" "GSM2631760" "GSM2631761" ...
## ..$ ReleaseDate : chr [1:6] "2017-07-05 17:24:20" "2017-07-05 17:24:20" "2017-07-05 17:24:20" "2017-07-05 17:24:20" ...
## ..$ LoadDate : chr [1:6] "2017-05-18 14:47:10" "2017-05-18 14:47:52" "2017-05-18 14:48:50" "2017-05-18 14:38:56" ...
## ..$ spots : int [1:6] 30694119 31940125 33870267 3149937 34013658 25700713
## ..$ bases : num [1:6] 6.14e+09 6.39e+09 6.77e+09 6.30e+08 6.80e+09 ...
## ..$ spots_with_mates : int [1:6] 30694119 31940125 33870267 3149937 34013658 25700713
## ..$ avgLength : int [1:6] 200 200 200 200 200 200
## ..$ size_MB : int [1:6] 3907 4051 4298 402 4336 3294
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5575722/SRR5575722.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5575723/SRR5575723.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5575724/SRR5575724.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5575725/SRR5575725.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP107327" "SRP107327" "SRP107327" "SRP107327" ...
## ..$ BioProject : chr [1:6] "PRJNA387175" "PRJNA387175" "PRJNA387175" "PRJNA387175" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 387175 387175 387175 387175 387175 387175
## ..$ Sample : chr [1:6] "SRS2208367" "SRS2208368" "SRS2208371" "SRS2208369" ...
## ..$ BioSample : chr [1:6] "SAMN07141092" "SAMN07141091" "SAMN07141090" "SAMN07141089" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA562554" "SRA562554" "SRA562554" "SRA562554" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "8199CE57A56C1B9DCBEB5FCC060BA7A7" "986417B95108F6DAB1CC725F0CA6510E" "343B785226E500B01B3E4980DA99E910" "F477A7E836AD29FE4B6F8A78ADF9A217" ...
## ..$ ReadHash : chr [1:6] "56E25823923C8A1CDC8FE624A25CBE07" "241E1136570F1AE7A90D50FFABC46740" "815120957568294A3F4A1ABD81DF784B" "C869C62CC313DB65436819B2E099BCDB" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP107327:control IL6Ra- versus IL6Ra+ in lean PBMC:IL6Ra-;SRX2833991,SRX2833993,SRX2833995,SRX2833997:IL6Ra+;SRX2833990,SRX2833992,SRX2833994,SRX2833996;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR5575728: int [1:58302] 0 0 4 0 0 0 0 0 0 0 ...
## ..$ SRR5575729: int [1:58302] 0 100 24 0 0 0 0 0 0 0 ...
## ..$ SRR5575730: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575731: int [1:58302] 0 102 18 0 0 0 0 0 0 0 ...
## ..$ SRR5575732: int [1:58302] 0 21 3 0 0 0 0 0 0 0 ...
## ..$ SRR5575733: int [1:58302] 0 57 15 0 0 0 0 0 0 0 ...
## ..$ SRR5575734: int [1:58302] 0 6 5 0 0 0 0 0 0 11 ...
## ..$ SRR5575735: int [1:58302] 0 94 13 0 0 0 0 2 0 13 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR5575728: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575729: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575730: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575731: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575732: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575733: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575734: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5575735: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR5575728: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575729: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575730: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575731: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575732: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575733: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575734: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5575735: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "FAIL(3,4,6)" "PASS" "FAIL(3,4,6)" "PASS" ...
## ..$ SRX_accession: chr [1:8] "SRX2833990" "SRX2833991" "SRX2833992" "SRX2833993" ...
## ..$ SRS_accession: chr [1:8] "SRS2208373" "SRS2208375" "SRS2208374" "SRS2208376" ...
## ..$ SRP_accession: chr [1:8] "SRP107327" "SRP107327" "SRP107327" "SRP107327" ...
## ..$ Sample_name : chr [1:8] "GSM2631764" "GSM2631765" "GSM2631766" "GSM2631767" ...
## ..$ GEO_series : chr [1:8] "GSE99068" "GSE99068" "GSE99068" "GSE99068" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "FAIL(3,4,6)" "PASS" "FAIL(3,4,6)" "PASS" ...
## ..$ SRX_accession : chr [1:8] "SRX2833990" "SRX2833991" "SRX2833992" "SRX2833993" ...
## ..$ SRS_accession : chr [1:8] "SRS2208373" "SRS2208375" "SRS2208374" "SRS2208376" ...
## ..$ SRP_accession : chr [1:8] "SRP107327" "SRP107327" "SRP107327" "SRP107327" ...
## ..$ Sample_name : chr [1:8] "GSM2631764" "GSM2631765" "GSM2631766" "GSM2631767" ...
## ..$ GEO_series : chr [1:8] "GSE99068" "GSE99068" "GSE99068" "GSE99068" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM2631764" "GSM2631765" "GSM2631766" "GSM2631767" ...
## ..$ ReleaseDate : chr [1:8] "2017-07-05 17:24:20" "2017-07-05 17:24:20" "2017-07-05 17:24:20" "2017-07-05 17:24:20" ...
## ..$ LoadDate : chr [1:8] "2017-05-18 14:48:31" "2017-05-18 15:02:16" "2017-05-18 14:42:35" "2017-05-18 14:51:23" ...
## ..$ spots : int [1:8] 28155709 33347987 10401896 31532964 29430635 33620386 33469297 25787022
## ..$ bases : num [1:8] 5.63e+09 6.67e+09 2.08e+09 6.31e+09 5.89e+09 ...
## ..$ spots_with_mates : int [1:8] 28155709 33347987 10401896 31532964 29430635 33620386 33469297 25787022
## ..$ avgLength : int [1:8] 200 200 200 200 200 200 200 200
## ..$ size_MB : int [1:8] 3614 4238 1370 3995 3765 4267 4267 3311
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5575728/SRR5575728.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5575729/SRR5575729.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5575730/SRR5575730.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5575731/SRR5575731.1" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:8] "SRP107327" "SRP107327" "SRP107327" "SRP107327" ...
## ..$ BioProject : chr [1:8] "PRJNA387175" "PRJNA387175" "PRJNA387175" "PRJNA387175" ...
## ..$ Study_Pubmed_id : int [1:8] 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:8] 387175 387175 387175 387175 387175 387175 387175 387175
## ..$ Sample : chr [1:8] "SRS2208373" "SRS2208375" "SRS2208374" "SRS2208376" ...
## ..$ BioSample : chr [1:8] "SAMN07141086" "SAMN07141085" "SAMN07141084" "SAMN07141083" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA562554" "SRA562554" "SRA562554" "SRA562554" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "463157BDC745DAD083DA135AC703955B" "903FD51B357D5A1733484216EC4D9654" "B2F38CE35C468A0C7F7CC10790C8EF23" "7C883CAF46AD79D26B167806F91FB5F5" ...
## ..$ ReadHash : chr [1:8] "A90C50FF4427BE66E36850DA6BDE3C6B" "97741DAA25DEF7EA2B6E2C5EDA98DB1C" "F97C3A0B303913E5D635A31F8191B36B" "48DFA06069A0DE7BB53E491E314D9AF0" ...
## $ absent : chr(0)## **SRP107327: obese PBMC versus lean PBMC:obese;SRX2833984,SRX2833985,SRX2833986,SRX2833987,SRX2833988,SRX2833989:lean;SRX2833990,SRX2833991,SRX2833992,SRX2833993,SRX2833994,SRX2833995,SRX2833996,SRX2833997;## Error. None of the specified SRR accessions are present.## NULL## SRP111557:non-diabetic versus Type II diabetic:non-diabetic;SRX2996334,SRX2996335,SRX2996336,SRX2996337,SRX2996338,SRX3413848:Type II diabetic;SRX2996339,SRX2996340,SRX3413849;sex,age,BMI## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR5818090: int [1:58302] 0 0 0 0 0 1 0 0 0 1 ...
## ..$ SRR5818091: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5818092: int [1:58302] 1 2 0 1 0 1 0 0 0 1 ...
## ..$ SRR5818093: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR5818094: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6313914: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR5818090: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5818091: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5818092: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5818093: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5818094: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6313914: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR5818090: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5818091: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5818092: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5818093: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5818094: chr [1:30] "PE" "Sanger/Illumina1.9" "26" "26" ...
## ..$ SRR6313914: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(3,4)" "FAIL(3,4)" "FAIL(3,4,6)" "FAIL(1,2)" ...
## ..$ SRX_accession: chr [1:6] "SRX2996336" "SRX2996337" "SRX2996338" "SRX2996339" ...
## ..$ SRS_accession: chr [1:6] "SRS2347568" "SRS2347569" "SRS2347570" "SRS2347571" ...
## ..$ SRP_accession: chr [1:6] "SRP111557" "SRP111557" "SRP111557" "SRP111557" ...
## ..$ Sample_name : chr [1:6] "GSM2700340" "GSM2700341" "GSM2700342" "GSM2700343" ...
## ..$ GEO_series : chr [1:6] "GSE101207" "GSE101207" "GSE101207" "GSE101207" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "FAIL(3,4)" "FAIL(3,4)" "FAIL(3,4,6)" "FAIL(1,2)" ...
## ..$ SRX_accession : chr [1:6] "SRX2996336" "SRX2996337" "SRX2996338" "SRX2996339" ...
## ..$ SRS_accession : chr [1:6] "SRS2347568" "SRS2347569" "SRS2347570" "SRS2347571" ...
## ..$ SRP_accession : chr [1:6] "SRP111557" "SRP111557" "SRP111557" "SRP111557" ...
## ..$ Sample_name : chr [1:6] "GSM2700340" "GSM2700341" "GSM2700342" "GSM2700343" ...
## ..$ GEO_series : chr [1:6] "GSE101207" "GSE101207" "GSE101207" "GSE101207" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2700340" "GSM2700341" "GSM2700342" "GSM2700343" ...
## ..$ ReleaseDate : chr [1:6] "2018-09-20 16:30:04" "2018-09-20 16:30:04" "2018-09-20 16:30:04" "2018-09-20 16:30:04" ...
## ..$ LoadDate : chr [1:6] "2017-07-11 19:14:46" "2017-07-11 18:55:16" "2017-07-11 19:02:14" "2017-07-11 18:36:45" ...
## ..$ spots : int [1:6] 99521732 54467641 86367370 12631020 64736964 45027210
## ..$ bases : num [1:6] 9.95e+09 5.45e+09 8.64e+09 1.26e+09 1.15e+10 ...
## ..$ spots_with_mates : int [1:6] 99521732 54467641 86367370 12631020 64736964 45027210
## ..$ avgLength : int [1:6] 100 100 100 100 177 100
## ..$ size_MB : int [1:6] 4244 2495 3590 555 4810 1686
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR5818090/SRR5818090.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR5818091/SRR5818091.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR5818092/SRR5818092.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR5818093/SRR5818093.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP111557" "SRP111557" "SRP111557" "SRP111557" ...
## ..$ BioProject : chr [1:6] "PRJNA393886" "PRJNA393886" "PRJNA393886" "PRJNA393886" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 393886 393886 393886 393886 393886 393886
## ..$ Sample : chr [1:6] "SRS2347568" "SRS2347569" "SRS2347570" "SRS2347571" ...
## ..$ BioSample : chr [1:6] "SAMN07343861" "SAMN07343860" "SAMN07343859" "SAMN07343858" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA585739" "SRA585739" "SRA585739" "SRA585739" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "9E68B962B3307CD865B63AC7AABC3B78" "AE82F04469613A0FC5C8CDA20FE59B68" "736F63139C5918451BF60F11E673B0EC" "D04D5C65E33BC8C754006412122F6F74" ...
## ..$ ReadHash : chr [1:6] "D5D70B37CBBEFB655BDAE355018B74D6" "28FA666EA769379F55C87D7CB0910CC3" "1E5AC3676E539EB882619138EA7FC40A" "F42F73D24AAEA553FB00D583A666B690" ...
## $ absent : chr(0)## SRP115040:normo-glycemic versus long duration type 1 diabetes:normo-glycemic;SRX3070956,SRX3070957,SRX3070958:long duration T1D;SRX3070959;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 7 variables:
## ..$ SRR5909500: int [1:58302] 0 64 4 1 0 0 0 0 0 0 ...
## ..$ SRR5909501: int [1:58302] 0 58 2 0 0 0 0 0 0 0 ...
## ..$ SRR5909502: int [1:58302] 0 345 14 0 0 0 0 0 0 2 ...
## ..$ SRR5909503: int [1:58302] 3 387 17 0 0 0 0 0 0 2 ...
## ..$ SRR5909504: int [1:58302] 0 57 4 0 0 0 0 0 0 11 ...
## ..$ SRR5909505: int [1:58302] 0 59 1 0 0 0 0 0 0 9 ...
## ..$ SRR5909507: int [1:58302] 0 123 16 0 0 0 0 0 0 4 ...
## $ TxCounts :'data.frame': 180869 obs. of 7 variables:
## ..$ SRR5909500: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909501: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909502: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909503: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909504: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909505: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909507: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 7 variables:
## ..$ SRR5909500: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909501: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909502: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909503: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909504: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909505: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909507: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 7 obs. of 7 variables:
## ..$ QC_summary : chr [1:7] "WARN(8)" "WARN(8)" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:7] "SRX3070956" "SRX3070956" "SRX3070957" "SRX3070957" ...
## ..$ SRS_accession: chr [1:7] "SRS2415287" "SRS2415287" "SRS2415286" "SRS2415286" ...
## ..$ SRP_accession: chr [1:7] "SRP115040" "SRP115040" "SRP115040" "SRP115040" ...
## ..$ Sample_name : chr [1:7] "GSM2735597" "GSM2735597" "GSM2735598" "GSM2735598" ...
## ..$ GEO_series : chr [1:7] "GSE102371" "GSE102371" "GSE102371" "GSE102371" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 7 obs. of 52 variables:
## ..$ QC_summary : chr [1:7] "WARN(8)" "WARN(8)" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:7] "SRX3070956" "SRX3070956" "SRX3070957" "SRX3070957" ...
## ..$ SRS_accession : chr [1:7] "SRS2415287" "SRS2415287" "SRS2415286" "SRS2415286" ...
## ..$ SRP_accession : chr [1:7] "SRP115040" "SRP115040" "SRP115040" "SRP115040" ...
## ..$ Sample_name : chr [1:7] "GSM2735597" "GSM2735597" "GSM2735598" "GSM2735598" ...
## ..$ GEO_series : chr [1:7] "GSE102371" "GSE102371" "GSE102371" "GSE102371" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:7] "GSM2735597" "GSM2735597" "GSM2735598" "GSM2735598" ...
## ..$ ReleaseDate : chr [1:7] "2018-07-31 09:14:28" "2018-07-31 09:14:28" "2018-07-31 09:14:28" "2018-07-31 09:14:28" ...
## ..$ LoadDate : chr [1:7] "2017-08-08 12:56:51" "2017-08-08 12:57:10" "2017-08-08 13:11:57" "2017-08-08 13:05:01" ...
## ..$ spots : int [1:7] 59908940 61132651 60678934 61616292 62229309 63390267 54942820
## ..$ bases : num [1:7] 1.21e+10 1.23e+10 1.23e+10 1.24e+10 1.26e+10 ...
## ..$ spots_with_mates : int [1:7] 59908940 61132651 60678934 61616292 62229309 63390267 54942820
## ..$ avgLength : int [1:7] 202 202 202 202 202 202 202
## ..$ size_MB : int [1:7] 4559 4616 4558 4591 4750 4820 4084
## ..$ AssemblyName : logi [1:7] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:7] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR5909500/SRR5909500.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR5909501/SRR5909501.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR5909502/SRR5909502.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR5909503/SRR5909503.1" ...
## ..$ LibraryName : logi [1:7] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:7] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:7] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:7] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:7] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:7] 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:7] 0 0 0 0 0 0 0
## ..$ Platform : chr [1:7] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:7] "Illumina HiSeq 3000" "Illumina HiSeq 3000" "Illumina HiSeq 3000" "Illumina HiSeq 3000" ...
## ..$ SRAStudy : chr [1:7] "SRP115040" "SRP115040" "SRP115040" "SRP115040" ...
## ..$ BioProject : chr [1:7] "PRJNA397581" "PRJNA397581" "PRJNA397581" "PRJNA397581" ...
## ..$ Study_Pubmed_id : int [1:7] 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:7] 397581 397581 397581 397581 397581 397581 397581
## ..$ Sample : chr [1:7] "SRS2415287" "SRS2415287" "SRS2415286" "SRS2415286" ...
## ..$ BioSample : chr [1:7] "SAMN07461313" "SAMN07461313" "SAMN07461312" "SAMN07461312" ...
## ..$ SampleType : chr [1:7] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:7] 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:7] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:7] NA NA NA NA NA NA ...
## ..$ source : logi [1:7] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:7] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:7] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:7] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:7] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:7] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:7] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:7] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:7] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:7] "SRA597509" "SRA597509" "SRA597509" "SRA597509" ...
## ..$ dbgap_study_accession: logi [1:7] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:7] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:7] "7331EE72E497886FB0EC0E1A29E572C1" "D9B3FD3A4AD57A28FF5335143769A769" "1C53EB021923CED0FA5E55E960439E5A" "E46E6874971A8FFFE23D3C84CF932912" ...
## ..$ ReadHash : chr [1:7] "96CD08704A4D9F76F69280C27B1D14DF" "ED2692DCE7B6A1B9202E09DD1749CE4D" "811A4B8F303C9ED922050198809448BA" "205DBCD77F28C1BC921A8177BE5BA82B" ...
## $ absent : chr(0)## SRP115040:normo-glycemic versus long duration type 1 diabetes:normo-glycemic;SRX3070956,SRX3070957,SRX3070958:short duration T1D;SRX3070960;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 7 variables:
## ..$ SRR5909500: int [1:58302] 0 64 4 1 0 0 0 0 0 0 ...
## ..$ SRR5909501: int [1:58302] 0 58 2 0 0 0 0 0 0 0 ...
## ..$ SRR5909502: int [1:58302] 0 345 14 0 0 0 0 0 0 2 ...
## ..$ SRR5909503: int [1:58302] 3 387 17 0 0 0 0 0 0 2 ...
## ..$ SRR5909504: int [1:58302] 0 57 4 0 0 0 0 0 0 11 ...
## ..$ SRR5909505: int [1:58302] 0 59 1 0 0 0 0 0 0 9 ...
## ..$ SRR5909509: int [1:58302] 0 54 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 7 variables:
## ..$ SRR5909500: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909501: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909502: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909503: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909504: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909505: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5909509: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 7 variables:
## ..$ SRR5909500: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909501: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909502: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909503: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909504: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909505: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5909509: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 7 obs. of 7 variables:
## ..$ QC_summary : chr [1:7] "WARN(8)" "WARN(8)" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:7] "SRX3070956" "SRX3070956" "SRX3070957" "SRX3070957" ...
## ..$ SRS_accession: chr [1:7] "SRS2415287" "SRS2415287" "SRS2415286" "SRS2415286" ...
## ..$ SRP_accession: chr [1:7] "SRP115040" "SRP115040" "SRP115040" "SRP115040" ...
## ..$ Sample_name : chr [1:7] "GSM2735597" "GSM2735597" "GSM2735598" "GSM2735598" ...
## ..$ GEO_series : chr [1:7] "GSE102371" "GSE102371" "GSE102371" "GSE102371" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 7 obs. of 52 variables:
## ..$ QC_summary : chr [1:7] "WARN(8)" "WARN(8)" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:7] "SRX3070956" "SRX3070956" "SRX3070957" "SRX3070957" ...
## ..$ SRS_accession : chr [1:7] "SRS2415287" "SRS2415287" "SRS2415286" "SRS2415286" ...
## ..$ SRP_accession : chr [1:7] "SRP115040" "SRP115040" "SRP115040" "SRP115040" ...
## ..$ Sample_name : chr [1:7] "GSM2735597" "GSM2735597" "GSM2735598" "GSM2735598" ...
## ..$ GEO_series : chr [1:7] "GSE102371" "GSE102371" "GSE102371" "GSE102371" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:7] "GSM2735597" "GSM2735597" "GSM2735598" "GSM2735598" ...
## ..$ ReleaseDate : chr [1:7] "2018-07-31 09:14:28" "2018-07-31 09:14:28" "2018-07-31 09:14:28" "2018-07-31 09:14:28" ...
## ..$ LoadDate : chr [1:7] "2017-08-08 12:56:51" "2017-08-08 12:57:10" "2017-08-08 13:11:57" "2017-08-08 13:05:01" ...
## ..$ spots : int [1:7] 59908940 61132651 60678934 61616292 62229309 63390267 61365412
## ..$ bases : num [1:7] 1.21e+10 1.23e+10 1.23e+10 1.24e+10 1.26e+10 ...
## ..$ spots_with_mates : int [1:7] 59908940 61132651 60678934 61616292 62229309 63390267 61365412
## ..$ avgLength : int [1:7] 202 202 202 202 202 202 202
## ..$ size_MB : int [1:7] 4559 4616 4558 4591 4750 4820 4685
## ..$ AssemblyName : logi [1:7] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:7] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR5909500/SRR5909500.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR5909501/SRR5909501.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR5909502/SRR5909502.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR5909503/SRR5909503.1" ...
## ..$ LibraryName : logi [1:7] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:7] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:7] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:7] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:7] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:7] 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:7] 0 0 0 0 0 0 0
## ..$ Platform : chr [1:7] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:7] "Illumina HiSeq 3000" "Illumina HiSeq 3000" "Illumina HiSeq 3000" "Illumina HiSeq 3000" ...
## ..$ SRAStudy : chr [1:7] "SRP115040" "SRP115040" "SRP115040" "SRP115040" ...
## ..$ BioProject : chr [1:7] "PRJNA397581" "PRJNA397581" "PRJNA397581" "PRJNA397581" ...
## ..$ Study_Pubmed_id : int [1:7] 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:7] 397581 397581 397581 397581 397581 397581 397581
## ..$ Sample : chr [1:7] "SRS2415287" "SRS2415287" "SRS2415286" "SRS2415286" ...
## ..$ BioSample : chr [1:7] "SAMN07461313" "SAMN07461313" "SAMN07461312" "SAMN07461312" ...
## ..$ SampleType : chr [1:7] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:7] 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:7] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:7] NA NA NA NA NA NA ...
## ..$ source : logi [1:7] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:7] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:7] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:7] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:7] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:7] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:7] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:7] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:7] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:7] "SRA597509" "SRA597509" "SRA597509" "SRA597509" ...
## ..$ dbgap_study_accession: logi [1:7] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:7] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:7] "7331EE72E497886FB0EC0E1A29E572C1" "D9B3FD3A4AD57A28FF5335143769A769" "1C53EB021923CED0FA5E55E960439E5A" "E46E6874971A8FFFE23D3C84CF932912" ...
## ..$ ReadHash : chr [1:7] "96CD08704A4D9F76F69280C27B1D14DF" "ED2692DCE7B6A1B9202E09DD1749CE4D" "811A4B8F303C9ED922050198809448BA" "205DBCD77F28C1BC921A8177BE5BA82B" ...
## $ absent : chr(0)## SRP144623:wild-type early stage pancreatic progenitors (PP1) versus wild-type late stage pancreatic progenitors (PP2):WP PP1;SRX4042188,SRX4042189:WT PP2;SRX4042190,SRX4042191,SRX4042192;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR7120589: int [1:58302] 0 0 0 2 0 0 0 0 0 0 ...
## ..$ SRR7120590: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120591: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120592: int [1:58302] 0 1 0 2 0 0 0 0 0 0 ...
## ..$ SRR7120593: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR7120589: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120590: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120591: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120592: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120593: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR7120589: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120590: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120591: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120592: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120593: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "PASS" "WARN(8)" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:5] "SRX4042188" "SRX4042189" "SRX4042190" "SRX4042191" ...
## ..$ SRS_accession: chr [1:5] "SRS3259641" "SRS3259642" "SRS3259643" "SRS3259644" ...
## ..$ SRP_accession: chr [1:5] "SRP144623" "SRP144623" "SRP144623" "SRP144623" ...
## ..$ Sample_name : chr [1:5] "GSM3131579" "GSM3131580" "GSM3131581" "GSM3131582" ...
## ..$ GEO_series : chr [1:5] "GSE114051" "GSE114051" "GSE114051" "GSE114051" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "PASS" "WARN(8)" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:5] "SRX4042188" "SRX4042189" "SRX4042190" "SRX4042191" ...
## ..$ SRS_accession : chr [1:5] "SRS3259641" "SRS3259642" "SRS3259643" "SRS3259644" ...
## ..$ SRP_accession : chr [1:5] "SRP144623" "SRP144623" "SRP144623" "SRP144623" ...
## ..$ Sample_name : chr [1:5] "GSM3131579" "GSM3131580" "GSM3131581" "GSM3131582" ...
## ..$ GEO_series : chr [1:5] "GSE114051" "GSE114051" "GSE114051" "GSE114051" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM3131579" "GSM3131580" "GSM3131581" "GSM3131582" ...
## ..$ ReleaseDate : chr [1:5] "2018-05-07 15:50:12" "2018-05-07 15:50:12" "2018-05-07 15:50:12" "2018-05-07 15:50:12" ...
## ..$ LoadDate : chr [1:5] "2018-05-04 17:55:50" "2018-05-04 17:58:17" "2018-05-04 17:57:22" "2018-05-04 17:58:22" ...
## ..$ spots : int [1:5] 28285619 32857352 30993737 37982333 41015635
## ..$ bases : int [1:5] 1442566569 1675724952 1580680587 1937098983 2091797385
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 51 51 51 51 51
## ..$ size_MB : int [1:5] 508 642 556 741 801
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120589/SRR7120589.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120590/SRR7120590.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120591/SRR7120591.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120592/SRR7120592.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:5] "SRP144623" "SRP144623" "SRP144623" "SRP144623" ...
## ..$ BioProject : chr [1:5] "PRJNA463329" "PRJNA463329" "PRJNA463329" "PRJNA463329" ...
## ..$ Study_Pubmed_id : int [1:5] 2 2 2 2 2
## ..$ ProjectID : int [1:5] 463329 463329 463329 463329 463329
## ..$ Sample : chr [1:5] "SRS3259641" "SRS3259642" "SRS3259643" "SRS3259644" ...
## ..$ BioSample : chr [1:5] "SAMN09071512" "SAMN09071511" "SAMN09071510" "SAMN09071509" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA699851" "SRA699851" "SRA699851" "SRA699851" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "2E8EE8453D6A361A2C6C9A3CF7330105" "8D06BCED32736DD51288EFA2B3C5E6E9" "7C5962032D6D8D15B0ABC42F3D70FEF6" "6747723CA4E1ECBD61082BE7A8CC203D" ...
## ..$ ReadHash : chr [1:5] "054539A04E5FA9448EB6D0E02B673D97" "15E48F71B5F5485DE070DC8581A359E0" "557DADE983379AD35AC0401E872DD506" "A9BA14FF0407AF92E8276F4383299A28" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP144623:wild-type late stage pancreatic progenitors (PP2) versus GLIS3-/- PP2:WT PP2;SRX4042190,SRX4042191,SRX4042192:GLIS3-/- PP2;SRX4042193,SRX4042194,SRX4042195;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR7120591: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120592: int [1:58302] 0 1 0 2 0 0 0 0 0 0 ...
## ..$ SRR7120593: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120594: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120595: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120596: int [1:58302] 0 5 0 1 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR7120591: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120592: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120593: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120594: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120595: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120596: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR7120591: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120592: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120593: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120594: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120595: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120596: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX4042190" "SRX4042191" "SRX4042192" "SRX4042193" ...
## ..$ SRS_accession: chr [1:6] "SRS3259643" "SRS3259644" "SRS3259645" "SRS3259646" ...
## ..$ SRP_accession: chr [1:6] "SRP144623" "SRP144623" "SRP144623" "SRP144623" ...
## ..$ Sample_name : chr [1:6] "GSM3131581" "GSM3131582" "GSM3131583" "GSM3131584" ...
## ..$ GEO_series : chr [1:6] "GSE114051" "GSE114051" "GSE114051" "GSE114051" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX4042190" "SRX4042191" "SRX4042192" "SRX4042193" ...
## ..$ SRS_accession : chr [1:6] "SRS3259643" "SRS3259644" "SRS3259645" "SRS3259646" ...
## ..$ SRP_accession : chr [1:6] "SRP144623" "SRP144623" "SRP144623" "SRP144623" ...
## ..$ Sample_name : chr [1:6] "GSM3131581" "GSM3131582" "GSM3131583" "GSM3131584" ...
## ..$ GEO_series : chr [1:6] "GSE114051" "GSE114051" "GSE114051" "GSE114051" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM3131581" "GSM3131582" "GSM3131583" "GSM3131584" ...
## ..$ ReleaseDate : chr [1:6] "2018-05-07 15:50:12" "2018-05-07 15:50:12" "2018-05-07 15:50:12" "2018-05-07 15:50:12" ...
## ..$ LoadDate : chr [1:6] "2018-05-04 17:57:22" "2018-05-04 17:58:22" "2018-05-04 17:58:07" "2018-05-04 17:54:31" ...
## ..$ spots : int [1:6] 30993737 37982333 41015635 25865486 36823751 43826246
## ..$ bases : num [1:6] 1.58e+09 1.94e+09 2.09e+09 1.32e+09 1.88e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 51 51 51 51 51 51
## ..$ size_MB : int [1:6] 556 741 801 466 727 863
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120591/SRR7120591.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120592/SRR7120592.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120593/SRR7120593.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120594/SRR7120594.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:6] "SRP144623" "SRP144623" "SRP144623" "SRP144623" ...
## ..$ BioProject : chr [1:6] "PRJNA463329" "PRJNA463329" "PRJNA463329" "PRJNA463329" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 463329 463329 463329 463329 463329 463329
## ..$ Sample : chr [1:6] "SRS3259643" "SRS3259644" "SRS3259645" "SRS3259646" ...
## ..$ BioSample : chr [1:6] "SAMN09071510" "SAMN09071509" "SAMN09071508" "SAMN09071521" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA699851" "SRA699851" "SRA699851" "SRA699851" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "7C5962032D6D8D15B0ABC42F3D70FEF6" "6747723CA4E1ECBD61082BE7A8CC203D" "2B4AD411A856A729AB481FD60467DBC2" "E3183F0DFBF82AE4DBD5B5C2F6BA3771" ...
## ..$ ReadHash : chr [1:6] "557DADE983379AD35AC0401E872DD506" "A9BA14FF0407AF92E8276F4383299A28" "9333C394E4E713456A3E9A80E8479C0E" "75DD0E98B1CCD6569B6448C7049F8EE7" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP144623:wild-type late stage pancreatic progenitors (PP2) versus WT INS-GFP+ PP2:WT PP2;SRX4042190,SRX4042191,SRX4042192:INS-GFP+ PP2;SRX4042198,SRX4042199;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR7120591: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120592: int [1:58302] 0 1 0 2 0 0 0 0 0 0 ...
## ..$ SRR7120593: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120599: int [1:58302] 0 9 0 2 0 0 0 0 0 0 ...
## ..$ SRR7120600: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR7120591: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120592: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120593: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120599: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120600: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR7120591: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120592: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120593: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120599: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120600: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:5] "SRX4042190" "SRX4042191" "SRX4042192" "SRX4042198" ...
## ..$ SRS_accession: chr [1:5] "SRS3259643" "SRS3259644" "SRS3259645" "SRS3259651" ...
## ..$ SRP_accession: chr [1:5] "SRP144623" "SRP144623" "SRP144623" "SRP144623" ...
## ..$ Sample_name : chr [1:5] "GSM3131581" "GSM3131582" "GSM3131583" "GSM3131589" ...
## ..$ GEO_series : chr [1:5] "GSE114051" "GSE114051" "GSE114051" "GSE114051" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:5] "SRX4042190" "SRX4042191" "SRX4042192" "SRX4042198" ...
## ..$ SRS_accession : chr [1:5] "SRS3259643" "SRS3259644" "SRS3259645" "SRS3259651" ...
## ..$ SRP_accession : chr [1:5] "SRP144623" "SRP144623" "SRP144623" "SRP144623" ...
## ..$ Sample_name : chr [1:5] "GSM3131581" "GSM3131582" "GSM3131583" "GSM3131589" ...
## ..$ GEO_series : chr [1:5] "GSE114051" "GSE114051" "GSE114051" "GSE114051" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM3131581" "GSM3131582" "GSM3131583" "GSM3131589" ...
## ..$ ReleaseDate : chr [1:5] "2018-05-07 15:50:12" "2018-05-07 15:50:12" "2018-05-07 15:50:12" "2018-05-07 15:50:12" ...
## ..$ LoadDate : chr [1:5] "2018-05-04 17:57:22" "2018-05-04 17:58:22" "2018-05-04 17:58:07" "2018-05-04 17:57:10" ...
## ..$ spots : int [1:5] 30993737 37982333 41015635 34710230 22118052
## ..$ bases : int [1:5] 1580680587 1937098983 2091797385 1770221730 1128020652
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 51 51 51 51 51
## ..$ size_MB : int [1:5] 556 741 801 630 403
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120591/SRR7120591.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120592/SRR7120592.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120593/SRR7120593.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120599/SRR7120599.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:5] "SRP144623" "SRP144623" "SRP144623" "SRP144623" ...
## ..$ BioProject : chr [1:5] "PRJNA463329" "PRJNA463329" "PRJNA463329" "PRJNA463329" ...
## ..$ Study_Pubmed_id : int [1:5] 2 2 2 2 2
## ..$ ProjectID : int [1:5] 463329 463329 463329 463329 463329
## ..$ Sample : chr [1:5] "SRS3259643" "SRS3259644" "SRS3259645" "SRS3259651" ...
## ..$ BioSample : chr [1:5] "SAMN09071510" "SAMN09071509" "SAMN09071508" "SAMN09071516" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA699851" "SRA699851" "SRA699851" "SRA699851" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "7C5962032D6D8D15B0ABC42F3D70FEF6" "6747723CA4E1ECBD61082BE7A8CC203D" "2B4AD411A856A729AB481FD60467DBC2" "801F73F788226FE9E4A08C0ED5192B6F" ...
## ..$ ReadHash : chr [1:5] "557DADE983379AD35AC0401E872DD506" "A9BA14FF0407AF92E8276F4383299A28" "9333C394E4E713456A3E9A80E8479C0E" "DD23C69B279B1AC29B77D1CFBB120FA5" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP144623:wild-type early stage pancreatic progenitors (PP1) versus WT INS-GFP+ PP1:WP PP1;SRX4042188,SRX4042189:WT INS-GFP+ PP1;SRX4042196,SRX4042197;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 4 variables:
## ..$ SRR7120589: int [1:58302] 0 0 0 2 0 0 0 0 0 0 ...
## ..$ SRR7120590: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120597: int [1:58302] 0 2 0 1 0 0 0 0 0 0 ...
## ..$ SRR7120598: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR7120589: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120590: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120597: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120598: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 4 variables:
## ..$ SRR7120589: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120590: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120597: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120598: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "WARN(8)" "WARN(3,4,8)" "WARN(8)"
## ..$ SRX_accession: chr [1:4] "SRX4042188" "SRX4042189" "SRX4042196" "SRX4042197"
## ..$ SRS_accession: chr [1:4] "SRS3259641" "SRS3259642" "SRS3259649" "SRS3259650"
## ..$ SRP_accession: chr [1:4] "SRP144623" "SRP144623" "SRP144623" "SRP144623"
## ..$ Sample_name : chr [1:4] "GSM3131579" "GSM3131580" "GSM3131587" "GSM3131588"
## ..$ GEO_series : chr [1:4] "GSE114051" "GSE114051" "GSE114051" "GSE114051"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "PASS" "WARN(8)" "WARN(3,4,8)" "WARN(8)"
## ..$ SRX_accession : chr [1:4] "SRX4042188" "SRX4042189" "SRX4042196" "SRX4042197"
## ..$ SRS_accession : chr [1:4] "SRS3259641" "SRS3259642" "SRS3259649" "SRS3259650"
## ..$ SRP_accession : chr [1:4] "SRP144623" "SRP144623" "SRP144623" "SRP144623"
## ..$ Sample_name : chr [1:4] "GSM3131579" "GSM3131580" "GSM3131587" "GSM3131588"
## ..$ GEO_series : chr [1:4] "GSE114051" "GSE114051" "GSE114051" "GSE114051"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM3131579" "GSM3131580" "GSM3131587" "GSM3131588"
## ..$ ReleaseDate : chr [1:4] "2018-05-07 15:50:12" "2018-05-07 15:50:12" "2018-05-07 15:50:12" "2018-05-07 15:50:12"
## ..$ LoadDate : chr [1:4] "2018-05-04 17:55:50" "2018-05-04 17:58:17" "2018-05-04 17:55:54" "2018-05-04 17:54:29"
## ..$ spots : int [1:4] 28285619 32857352 43962185 45850152
## ..$ bases : num [1:4] 1.44e+09 1.68e+09 2.24e+09 2.34e+09
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 51 51 51 51
## ..$ size_MB : int [1:4] 508 642 1440 1501
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120589/SRR7120589.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120590/SRR7120590.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120597/SRR7120597.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120598/SRR7120598.1"
## ..$ LibraryName : logi [1:4] NA NA NA NA
## ..$ LibraryStrategy : chr [1:4] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq"
## ..$ LibrarySelection : chr [1:4] "cDNA" "cDNA" "cDNA" "cDNA"
## ..$ LibrarySource : chr [1:4] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr [1:4] "SINGLE" "SINGLE" "SINGLE" "SINGLE"
## ..$ InsertSize : int [1:4] 0 0 0 0
## ..$ InsertDev : num [1:4] 0 0 0 0
## ..$ Platform : chr [1:4] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA"
## ..$ Model : chr [1:4] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000"
## ..$ SRAStudy : chr [1:4] "SRP144623" "SRP144623" "SRP144623" "SRP144623"
## ..$ BioProject : chr [1:4] "PRJNA463329" "PRJNA463329" "PRJNA463329" "PRJNA463329"
## ..$ Study_Pubmed_id : int [1:4] 2 2 2 2
## ..$ ProjectID : int [1:4] 463329 463329 463329 463329
## ..$ Sample : chr [1:4] "SRS3259641" "SRS3259642" "SRS3259649" "SRS3259650"
## ..$ BioSample : chr [1:4] "SAMN09071512" "SAMN09071511" "SAMN09071518" "SAMN09071517"
## ..$ SampleType : chr [1:4] "simple" "simple" "simple" "simple"
## ..$ TaxID : int [1:4] 9606 9606 9606 9606
## ..$ ScientificName : chr [1:4] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"
## ..$ g1k_pop_code : logi [1:4] NA NA NA NA
## ..$ source : logi [1:4] NA NA NA NA
## ..$ g1k_analysis_group : logi [1:4] NA NA NA NA
## ..$ Subject_ID : logi [1:4] NA NA NA NA
## ..$ Sex : logi [1:4] NA NA NA NA
## ..$ Disease : logi [1:4] NA NA NA NA
## ..$ Tumor : chr [1:4] "no" "no" "no" "no"
## ..$ Affection_Status : logi [1:4] NA NA NA NA
## ..$ Analyte_Type : logi [1:4] NA NA NA NA
## ..$ Histological_Type : logi [1:4] NA NA NA NA
## ..$ Body_Site : logi [1:4] NA NA NA NA
## ..$ CenterName : chr [1:4] "GEO" "GEO" "GEO" "GEO"
## ..$ Submission : chr [1:4] "SRA699851" "SRA699851" "SRA699851" "SRA699851"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "2E8EE8453D6A361A2C6C9A3CF7330105" "8D06BCED32736DD51288EFA2B3C5E6E9" "C848C00DC931CAFEB6884913BAF13488" "4B9EA191E2DB2C26261B52771AF092CD"
## ..$ ReadHash : chr [1:4] "054539A04E5FA9448EB6D0E02B673D97" "15E48F71B5F5485DE070DC8581A359E0" "04D5ECF08BA2B77154DF62478503A04C" "8A639F09F18F8832FF6663A55A16E696"
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP144623:GLIS3 PP2 versus GLIS3-/- INS-GFPT PP2:GLIS3 PP2;SRX4042193,SRX4042194,SRX4042195:GLIS3-/- INS-GFPT PP2;SRX4042200,SRX4042201;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 4 variables:
## ..$ SRR7120594: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120595: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120596: int [1:58302] 0 5 0 1 0 0 0 0 0 0 ...
## ..$ SRR7120602: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR7120594: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120595: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120596: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7120602: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 4 variables:
## ..$ SRR7120594: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120595: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120596: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7120602: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "PASS" "WARN(8)"
## ..$ SRX_accession: chr [1:4] "SRX4042193" "SRX4042194" "SRX4042195" "SRX4042201"
## ..$ SRS_accession: chr [1:4] "SRS3259646" "SRS3259647" "SRS3259648" "SRS3259654"
## ..$ SRP_accession: chr [1:4] "SRP144623" "SRP144623" "SRP144623" "SRP144623"
## ..$ Sample_name : chr [1:4] "GSM3131584" "GSM3131585" "GSM3131586" "GSM3131592"
## ..$ GEO_series : chr [1:4] "GSE114051" "GSE114051" "GSE114051" "GSE114051"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "PASS" "WARN(8)"
## ..$ SRX_accession : chr [1:4] "SRX4042193" "SRX4042194" "SRX4042195" "SRX4042201"
## ..$ SRS_accession : chr [1:4] "SRS3259646" "SRS3259647" "SRS3259648" "SRS3259654"
## ..$ SRP_accession : chr [1:4] "SRP144623" "SRP144623" "SRP144623" "SRP144623"
## ..$ Sample_name : chr [1:4] "GSM3131584" "GSM3131585" "GSM3131586" "GSM3131592"
## ..$ GEO_series : chr [1:4] "GSE114051" "GSE114051" "GSE114051" "GSE114051"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM3131584" "GSM3131585" "GSM3131586" "GSM3131592"
## ..$ ReleaseDate : chr [1:4] "2018-05-07 15:50:12" "2018-05-07 15:50:12" "2018-05-07 15:50:12" "2018-05-07 15:50:13"
## ..$ LoadDate : chr [1:4] "2018-05-04 17:54:31" "2018-05-04 17:56:55" "2018-05-04 18:03:21" "2018-05-04 17:58:12"
## ..$ spots : int [1:4] 25865486 36823751 43826246 30440357
## ..$ bases : num [1:4] 1.32e+09 1.88e+09 2.24e+09 1.55e+09
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 51 51 51 51
## ..$ size_MB : int [1:4] 466 727 863 547
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120594/SRR7120594.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120595/SRR7120595.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120596/SRR7120596.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-13/SRR7120602/SRR7120602.1"
## ..$ LibraryName : logi [1:4] NA NA NA NA
## ..$ LibraryStrategy : chr [1:4] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq"
## ..$ LibrarySelection : chr [1:4] "cDNA" "cDNA" "cDNA" "cDNA"
## ..$ LibrarySource : chr [1:4] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr [1:4] "SINGLE" "SINGLE" "SINGLE" "SINGLE"
## ..$ InsertSize : int [1:4] 0 0 0 0
## ..$ InsertDev : num [1:4] 0 0 0 0
## ..$ Platform : chr [1:4] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA"
## ..$ Model : chr [1:4] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000"
## ..$ SRAStudy : chr [1:4] "SRP144623" "SRP144623" "SRP144623" "SRP144623"
## ..$ BioProject : chr [1:4] "PRJNA463329" "PRJNA463329" "PRJNA463329" "PRJNA463329"
## ..$ Study_Pubmed_id : int [1:4] 2 2 2 2
## ..$ ProjectID : int [1:4] 463329 463329 463329 463329
## ..$ Sample : chr [1:4] "SRS3259646" "SRS3259647" "SRS3259648" "SRS3259654"
## ..$ BioSample : chr [1:4] "SAMN09071521" "SAMN09071520" "SAMN09071519" "SAMN09071513"
## ..$ SampleType : chr [1:4] "simple" "simple" "simple" "simple"
## ..$ TaxID : int [1:4] 9606 9606 9606 9606
## ..$ ScientificName : chr [1:4] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens"
## ..$ g1k_pop_code : logi [1:4] NA NA NA NA
## ..$ source : logi [1:4] NA NA NA NA
## ..$ g1k_analysis_group : logi [1:4] NA NA NA NA
## ..$ Subject_ID : logi [1:4] NA NA NA NA
## ..$ Sex : logi [1:4] NA NA NA NA
## ..$ Disease : logi [1:4] NA NA NA NA
## ..$ Tumor : chr [1:4] "no" "no" "no" "no"
## ..$ Affection_Status : logi [1:4] NA NA NA NA
## ..$ Analyte_Type : logi [1:4] NA NA NA NA
## ..$ Histological_Type : logi [1:4] NA NA NA NA
## ..$ Body_Site : logi [1:4] NA NA NA NA
## ..$ CenterName : chr [1:4] "GEO" "GEO" "GEO" "GEO"
## ..$ Submission : chr [1:4] "SRA699851" "SRA699851" "SRA699851" "SRA699851"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "E3183F0DFBF82AE4DBD5B5C2F6BA3771" "6918F65E61D56226D2BED7EF49C60CAC" "F0016B249A69DE530E2A9BB924629557" "FADFA813E94155F1821822CC1EDA4952"
## ..$ ReadHash : chr [1:4] "75DD0E98B1CCD6569B6448C7049F8EE7" "AF7B6400BB9ABC4DA190F3DCA01F680F" "D770F9DB171546594DECCDD9C81B4B56" "8012C6AC27A43D36224C73EB4D90CEDD"
## $ absent : chr(0)## SRP154717:pericytes cultured in control versus diabetic:control;SRX4415408,SRX4415409,SRX4415410,SRX4415417,SRX4415418,SRX4415419:diabetic;SRX4415423,SRX4415424,SRX4415425;sex
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR7549232: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549242: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549247: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549248: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549249: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR7549232: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549242: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549247: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549248: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549249: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR7549232: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549242: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549247: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549248: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549249: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "WARN(1,5,7,8)" "FAIL(5,7)" "WARN(1,5,7)" "WARN(1,4,5,7)" ...
## ..$ SRX_accession: chr [1:5] "SRX4415408" "SRX4415418" "SRX4415423" "SRX4415424" ...
## ..$ SRS_accession: chr [1:5] "SRS3568683" "SRS3568693" "SRS3568698" "SRS3568699" ...
## ..$ SRP_accession: chr [1:5] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ Sample_name : chr [1:5] "GSM3301483" "GSM3301493" "GSM3301498" "GSM3301499" ...
## ..$ GEO_series : chr [1:5] "GSE117469" "GSE117469" "GSE117469" "GSE117469" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "WARN(1,5,7,8)" "FAIL(5,7)" "WARN(1,5,7)" "WARN(1,4,5,7)" ...
## ..$ SRX_accession : chr [1:5] "SRX4415408" "SRX4415418" "SRX4415423" "SRX4415424" ...
## ..$ SRS_accession : chr [1:5] "SRS3568683" "SRS3568693" "SRS3568698" "SRS3568699" ...
## ..$ SRP_accession : chr [1:5] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ Sample_name : chr [1:5] "GSM3301483" "GSM3301493" "GSM3301498" "GSM3301499" ...
## ..$ GEO_series : chr [1:5] "GSE117469" "GSE117469" "GSE117469" "GSE117469" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM3301483" "GSM3301493" "GSM3301498" "GSM3301499" ...
## ..$ ReleaseDate : chr [1:5] "2018-10-31 16:47:04" "2018-10-31 16:47:04" "2018-10-31 16:47:04" "2018-10-31 16:47:04" ...
## ..$ LoadDate : chr [1:5] "2018-07-22 13:09:41" "2018-07-22 13:09:35" "2018-07-22 13:09:53" "2018-07-22 13:09:41" ...
## ..$ spots : int [1:5] 2467604 1228947 3160177 2068617 2443088
## ..$ bases : int [1:5] 123380200 61447350 158008850 103430850 122154400
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 50 50 50 50 50
## ..$ size_MB : int [1:5] 46 26 60 40 47
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-download.ncbi.nlm.nih.gov/traces/sra68/SRR/007372/SRR7549232" "https://sra-download.ncbi.nlm.nih.gov/traces/sra65/SRR/007372/SRR7549242" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7549247/SRR7549247.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/007372/SRR7549248" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:5] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ BioProject : chr [1:5] "PRJNA482245" "PRJNA482245" "PRJNA482245" "PRJNA482245" ...
## ..$ Study_Pubmed_id : int [1:5] 3 3 3 3 3
## ..$ ProjectID : int [1:5] 482245 482245 482245 482245 482245
## ..$ Sample : chr [1:5] "SRS3568683" "SRS3568693" "SRS3568698" "SRS3568699" ...
## ..$ BioSample : chr [1:5] "SAMN09701118" "SAMN09701108" "SAMN09701103" "SAMN09701135" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA743491" "SRA743491" "SRA743491" "SRA743491" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "3A7547CB5460D1FD5FBFC1FC0A115FA7" "8F049A3CDCC7D68F5C9C734A270EBF28" "29F299D7C3635983E3781512111F5093" "D85199CABA71F485601450F558F69435" ...
## ..$ ReadHash : chr [1:5] "6D9D55D3658361918499AA0FDCE0AB2D" "E116C25F02C1003E26556D8566AC9886" "87503C77D4F08A22C24979C5CB1E58DE" "FF7D71C22AAC97DAF5CDA1118BD61D38" ...
## $ absent : chr(0)## SRP154717:pericytes cultured in diabetic versus pDAPT:diabetic;SRX4415423,SRX4415424,SRX4415425:pDAPT;SRX4415429,SRX4415430,SRX4415431;sex
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR7549247: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549248: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549249: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549254: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549255: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR7549247: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549248: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549249: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549254: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549255: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR7549247: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549248: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549249: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549254: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549255: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "WARN(1,5,7)" "WARN(1,4,5,7)" "WARN(1,5,7)" "WARN(1,4,5,7)" ...
## ..$ SRX_accession: chr [1:5] "SRX4415423" "SRX4415424" "SRX4415425" "SRX4415430" ...
## ..$ SRS_accession: chr [1:5] "SRS3568698" "SRS3568699" "SRS3568700" "SRS3568705" ...
## ..$ SRP_accession: chr [1:5] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ Sample_name : chr [1:5] "GSM3301498" "GSM3301499" "GSM3301500" "GSM3301505" ...
## ..$ GEO_series : chr [1:5] "GSE117469" "GSE117469" "GSE117469" "GSE117469" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "WARN(1,5,7)" "WARN(1,4,5,7)" "WARN(1,5,7)" "WARN(1,4,5,7)" ...
## ..$ SRX_accession : chr [1:5] "SRX4415423" "SRX4415424" "SRX4415425" "SRX4415430" ...
## ..$ SRS_accession : chr [1:5] "SRS3568698" "SRS3568699" "SRS3568700" "SRS3568705" ...
## ..$ SRP_accession : chr [1:5] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ Sample_name : chr [1:5] "GSM3301498" "GSM3301499" "GSM3301500" "GSM3301505" ...
## ..$ GEO_series : chr [1:5] "GSE117469" "GSE117469" "GSE117469" "GSE117469" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM3301498" "GSM3301499" "GSM3301500" "GSM3301505" ...
## ..$ ReleaseDate : chr [1:5] "2018-10-31 16:47:04" "2018-10-31 16:47:04" "2018-10-31 16:47:04" "2018-10-31 16:47:05" ...
## ..$ LoadDate : chr [1:5] "2018-07-22 13:09:53" "2018-07-22 13:09:41" "2018-07-22 13:09:49" "2018-07-22 13:09:51" ...
## ..$ spots : int [1:5] 3160177 2068617 2443088 2589342 2037095
## ..$ bases : int [1:5] 158008850 103430850 122154400 129467100 101854750
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 50 50 50 50 50
## ..$ size_MB : int [1:5] 60 40 47 49 38
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7549247/SRR7549247.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/007372/SRR7549248" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/007372/SRR7549249" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7549254/SRR7549254.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:5] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ BioProject : chr [1:5] "PRJNA482245" "PRJNA482245" "PRJNA482245" "PRJNA482245" ...
## ..$ Study_Pubmed_id : int [1:5] 3 3 3 3 3
## ..$ ProjectID : int [1:5] 482245 482245 482245 482245 482245
## ..$ Sample : chr [1:5] "SRS3568698" "SRS3568699" "SRS3568700" "SRS3568705" ...
## ..$ BioSample : chr [1:5] "SAMN09701103" "SAMN09701135" "SAMN09701134" "SAMN09701129" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA743491" "SRA743491" "SRA743491" "SRA743491" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "29F299D7C3635983E3781512111F5093" "D85199CABA71F485601450F558F69435" "A1C6CAB085BB205C465F1B1DDF975A55" "5D85AF78070FD49B35EAED8C7509772D" ...
## ..$ ReadHash : chr [1:5] "87503C77D4F08A22C24979C5CB1E58DE" "FF7D71C22AAC97DAF5CDA1118BD61D38" "59E31CEFB54645D97B99F9282F3808C6" "FD3A9934DB707E37E7353F5B112B5B24" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP154717:endothelial cell cultured in control versus diabetic:control;SRX4415405,SRX4415406,SRX4415407,SRX4415414,SRX4415415,SRX4415416:diabetic;SRX4415420,SRX4415421,SRX4415422;sex## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 7 variables:
## ..$ SRR7549229: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549230: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549238: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549239: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549240: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549245: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549246: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 7 variables:
## ..$ SRR7549229: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549230: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549238: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549239: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549240: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549245: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549246: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 7 variables:
## ..$ SRR7549229: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549230: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549238: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549239: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549240: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549245: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549246: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 7 obs. of 7 variables:
## ..$ QC_summary : chr [1:7] "WARN(1,5,7)" "FAIL(5,7)" "WARN(1,5,7)" "WARN(1,4,5,6,7)" ...
## ..$ SRX_accession: chr [1:7] "SRX4415405" "SRX4415406" "SRX4415414" "SRX4415415" ...
## ..$ SRS_accession: chr [1:7] "SRS3568680" "SRS3568681" "SRS3568689" "SRS3568690" ...
## ..$ SRP_accession: chr [1:7] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ Sample_name : chr [1:7] "GSM3301480" "GSM3301481" "GSM3301489" "GSM3301490" ...
## ..$ GEO_series : chr [1:7] "GSE117469" "GSE117469" "GSE117469" "GSE117469" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 7 obs. of 52 variables:
## ..$ QC_summary : chr [1:7] "WARN(1,5,7)" "FAIL(5,7)" "WARN(1,5,7)" "WARN(1,4,5,6,7)" ...
## ..$ SRX_accession : chr [1:7] "SRX4415405" "SRX4415406" "SRX4415414" "SRX4415415" ...
## ..$ SRS_accession : chr [1:7] "SRS3568680" "SRS3568681" "SRS3568689" "SRS3568690" ...
## ..$ SRP_accession : chr [1:7] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ Sample_name : chr [1:7] "GSM3301480" "GSM3301481" "GSM3301489" "GSM3301490" ...
## ..$ GEO_series : chr [1:7] "GSE117469" "GSE117469" "GSE117469" "GSE117469" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:7] "GSM3301480" "GSM3301481" "GSM3301489" "GSM3301490" ...
## ..$ ReleaseDate : chr [1:7] "2018-10-31 16:47:04" "2018-10-31 16:47:04" "2018-10-31 16:47:04" "2018-10-31 16:47:04" ...
## ..$ LoadDate : chr [1:7] "2018-07-22 13:09:32" "2018-07-22 13:09:30" "2018-07-22 13:09:52" "2018-07-22 13:10:12" ...
## ..$ spots : int [1:7] 1923455 1166311 3461948 5034470 3537999 2877282 2571055
## ..$ bases : int [1:7] 96172750 58315550 173097400 251723500 176899950 143864100 128552750
## ..$ spots_with_mates : int [1:7] 0 0 0 0 0 0 0
## ..$ avgLength : int [1:7] 50 50 50 50 50 50 50
## ..$ size_MB : int [1:7] 38 24 65 94 67 55 51
## ..$ AssemblyName : logi [1:7] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:7] "https://sra-download.ncbi.nlm.nih.gov/traces/sra65/SRR/007372/SRR7549229" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/007372/SRR7549230" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7549238/SRR7549238.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7549239/SRR7549239.1" ...
## ..$ LibraryName : logi [1:7] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:7] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:7] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:7] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:7] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:7] 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:7] 0 0 0 0 0 0 0
## ..$ Platform : chr [1:7] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:7] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:7] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ BioProject : chr [1:7] "PRJNA482245" "PRJNA482245" "PRJNA482245" "PRJNA482245" ...
## ..$ Study_Pubmed_id : int [1:7] 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:7] 482245 482245 482245 482245 482245 482245 482245
## ..$ Sample : chr [1:7] "SRS3568680" "SRS3568681" "SRS3568689" "SRS3568690" ...
## ..$ BioSample : chr [1:7] "SAMN09701121" "SAMN09701120" "SAMN09701112" "SAMN09701111" ...
## ..$ SampleType : chr [1:7] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:7] 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:7] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:7] NA NA NA NA NA NA ...
## ..$ source : logi [1:7] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:7] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:7] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:7] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:7] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:7] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:7] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:7] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:7] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:7] "SRA743491" "SRA743491" "SRA743491" "SRA743491" ...
## ..$ dbgap_study_accession: logi [1:7] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:7] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:7] "0445346C362C1C7576E1D2F30891652F" "A73EF93F939BE1F8AD07D26619F72402" "B896467C26B9DBD61CC52B398A300538" "41AD4708E2CEF6EDF4C5BE479316BE84" ...
## ..$ ReadHash : chr [1:7] "D44B04C4EEAACC933C5EE4CB6050D983" "8776E2F6378408B9CF9C3F00EC3F979A" "3BB869CACB42E2F77D93FFE8CD6E172A" "1851F5193847035FA8F57EF2F4E61E8E" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP154717:endothelial cell cultured in diabetic versus pDAPT:diabetic;SRX4415420,SRX4415421,SRX4415422:pDAPT;SRX4415426,SRX4415427,SRX4415428;sex## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR7549245: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549246: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549250: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549251: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549252: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR7549245: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549246: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549250: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549251: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7549252: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR7549245: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549246: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549250: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549251: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7549252: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "WARN(1,4,5,7)" "WARN(1,4,5,7)" "WARN(1,4,5,7)" "FAIL(5)" ...
## ..$ SRX_accession: chr [1:5] "SRX4415421" "SRX4415422" "SRX4415426" "SRX4415427" ...
## ..$ SRS_accession: chr [1:5] "SRS3568695" "SRS3568697" "SRS3568701" "SRS3568702" ...
## ..$ SRP_accession: chr [1:5] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ Sample_name : chr [1:5] "GSM3301496" "GSM3301497" "GSM3301501" "GSM3301502" ...
## ..$ GEO_series : chr [1:5] "GSE117469" "GSE117469" "GSE117469" "GSE117469" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "WARN(1,4,5,7)" "WARN(1,4,5,7)" "WARN(1,4,5,7)" "FAIL(5)" ...
## ..$ SRX_accession : chr [1:5] "SRX4415421" "SRX4415422" "SRX4415426" "SRX4415427" ...
## ..$ SRS_accession : chr [1:5] "SRS3568695" "SRS3568697" "SRS3568701" "SRS3568702" ...
## ..$ SRP_accession : chr [1:5] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ Sample_name : chr [1:5] "GSM3301496" "GSM3301497" "GSM3301501" "GSM3301502" ...
## ..$ GEO_series : chr [1:5] "GSE117469" "GSE117469" "GSE117469" "GSE117469" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM3301496" "GSM3301497" "GSM3301501" "GSM3301502" ...
## ..$ ReleaseDate : chr [1:5] "2018-10-31 16:47:04" "2018-10-31 16:47:04" "2018-10-31 16:47:04" "2018-10-31 16:47:04" ...
## ..$ LoadDate : chr [1:5] "2018-07-22 13:09:49" "2018-07-22 13:09:49" "2018-07-22 13:09:47" "2018-07-22 13:09:42" ...
## ..$ spots : int [1:5] 2877282 2571055 2059436 1570109 4222575
## ..$ bases : int [1:5] 143864100 128552750 102971800 78505450 211128750
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 50 50 50 50 50
## ..$ size_MB : int [1:5] 55 51 39 29 79
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/007372/SRR7549245" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7549246/SRR7549246.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/007372/SRR7549250" "https://sra-download.ncbi.nlm.nih.gov/traces/sra65/SRR/007372/SRR7549251" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:5] "SRP154717" "SRP154717" "SRP154717" "SRP154717" ...
## ..$ BioProject : chr [1:5] "PRJNA482245" "PRJNA482245" "PRJNA482245" "PRJNA482245" ...
## ..$ Study_Pubmed_id : int [1:5] 3 3 3 3 3
## ..$ ProjectID : int [1:5] 482245 482245 482245 482245 482245
## ..$ Sample : chr [1:5] "SRS3568695" "SRS3568697" "SRS3568701" "SRS3568702" ...
## ..$ BioSample : chr [1:5] "SAMN09701105" "SAMN09701104" "SAMN09701133" "SAMN09701132" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA743491" "SRA743491" "SRA743491" "SRA743491" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "135342E35D88A3A98806FA0C6F70A0E0" "9B9BE286DD2D5590F4D3092095EFAD25" "3C3DC85E7CA2BE3339D34B95B45B353F" "0519F068841638F031B0244C04142A7E" ...
## ..$ ReadHash : chr [1:5] "52F953E0E6C5D655F817F6FFCCA37263" "C58BFFF682DEB284AA35485ABCDDE549" "DEE4ACE04A40A658826673E5E47764AB" "5BDDD998ED0247F83D57F2C66FA9CB4F" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP163900:UN (untreated) versus IL15 in ex vivo:UN;SRX4804447,SRX4804454,SRX4804461,SRX4804468,SRX4804475:IL15;SRX4804441,SRX4804448,SRX4804455,SRX4804462,SRX4804469;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR7971405: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971411: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971412: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971418: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971419: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971425: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971426: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971432: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971433: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971439: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR7971405: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971411: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971412: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971418: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971419: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971425: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971426: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971432: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971433: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971439: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR7971405: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971411: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971412: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971418: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971419: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971425: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971426: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971432: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971433: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971439: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "FAIL(4,6)" "FAIL(1,2,3,4,5,6,7)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession: chr [1:10] "SRX4804441" "SRX4804447" "SRX4804448" "SRX4804454" ...
## ..$ SRS_accession: chr [1:10] "SRS3883131" "SRS3883137" "SRS3883138" "SRS3883144" ...
## ..$ SRP_accession: chr [1:10] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:10] "GSM3418205" "GSM3418211" "GSM3418212" "GSM3418218" ...
## ..$ GEO_series : chr [1:10] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "FAIL(4,6)" "FAIL(1,2,3,4,5,6,7)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession : chr [1:10] "SRX4804441" "SRX4804447" "SRX4804448" "SRX4804454" ...
## ..$ SRS_accession : chr [1:10] "SRS3883131" "SRS3883137" "SRS3883138" "SRS3883144" ...
## ..$ SRP_accession : chr [1:10] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:10] "GSM3418205" "GSM3418211" "GSM3418212" "GSM3418218" ...
## ..$ GEO_series : chr [1:10] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM3418205" "GSM3418211" "GSM3418212" "GSM3418218" ...
## ..$ ReleaseDate : chr [1:10] "2018-10-08 18:32:27" "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" ...
## ..$ LoadDate : chr [1:10] "2018-10-05 17:39:18" "2018-10-05 17:40:49" "2018-10-05 17:42:41" "2018-10-05 17:42:10" ...
## ..$ spots : int [1:10] 16698270 21139720 21133448 19838533 16118899 19404043 21776546 17862895 22240028 22338230
## ..$ bases : int [1:10] 834913500 1056986000 1056672400 991926650 805944950 970202150 1088827300 893144750 1112001400 1116911500
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 50 50 50 50 50 50 50 50 50 50
## ..$ size_MB : int [1:10] 285 360 360 338 275 329 371 304 379 381
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971405" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971411/SRR7971411.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971412" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971418" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:10] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 494882 494882 494882 494882 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:10] "SRS3883131" "SRS3883137" "SRS3883138" "SRS3883144" ...
## ..$ BioSample : chr [1:10] "SAMN10182830" "SAMN10182824" "SAMN10182823" "SAMN10182817" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "933DEF81DFC64DB4A639103B1E72624D" "5A885C068A3E0EA8572E5A149C2E21E5" "92EC35C1FE7FDD892EC41E6DC2E6EFEF" "0F420CD37A17545F4931051DB2780696" ...
## ..$ ReadHash : chr [1:10] "6A19F6D7640CA1BD3FE383E59275E87B" "14BCD07846B0101F53EEA56CB90CCACB" "1AE6117C82EE9B0BD10EE9865AD1BE6B" "8F85718181702F31869A2C8E7848E21E" ...
## $ absent : chr(0)## SRP163900:IL15 versus IL15+BNZ in ex vivo:IL15;SRX4804441,SRX4804448,SRX4804455,SRX4804462,SRX4804469:IL15+BNZ;SRX4804442,SRX4804449,SRX4804456,SRX4804463,SRX4804470;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR7971405: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971406: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971412: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971413: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971419: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971426: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971427: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971433: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR7971405: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971406: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971412: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971413: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971419: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971426: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971427: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971433: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR7971405: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971406: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971412: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971413: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971419: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971426: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971427: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971433: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession: chr [1:8] "SRX4804441" "SRX4804442" "SRX4804448" "SRX4804449" ...
## ..$ SRS_accession: chr [1:8] "SRS3883131" "SRS3883132" "SRS3883138" "SRS3883139" ...
## ..$ SRP_accession: chr [1:8] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:8] "GSM3418205" "GSM3418206" "GSM3418212" "GSM3418213" ...
## ..$ GEO_series : chr [1:8] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession : chr [1:8] "SRX4804441" "SRX4804442" "SRX4804448" "SRX4804449" ...
## ..$ SRS_accession : chr [1:8] "SRS3883131" "SRS3883132" "SRS3883138" "SRS3883139" ...
## ..$ SRP_accession : chr [1:8] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:8] "GSM3418205" "GSM3418206" "GSM3418212" "GSM3418213" ...
## ..$ GEO_series : chr [1:8] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM3418205" "GSM3418206" "GSM3418212" "GSM3418213" ...
## ..$ ReleaseDate : chr [1:8] "2018-10-08 18:32:27" "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" ...
## ..$ LoadDate : chr [1:8] "2018-10-05 17:39:18" "2018-10-05 17:41:16" "2018-10-05 17:42:41" "2018-10-05 17:41:02" ...
## ..$ spots : int [1:8] 16698270 21837559 21133448 18519110 16118899 21776546 19579057 22240028
## ..$ bases : int [1:8] 834913500 1091877950 1056672400 925955500 805944950 1088827300 978952850 1112001400
## ..$ spots_with_mates : int [1:8] 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:8] 50 50 50 50 50 50 50 50
## ..$ size_MB : int [1:8] 285 371 360 316 275 371 333 379
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971405" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971406/SRR7971406.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971412" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971413/SRR7971413.1" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:8] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:8] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:8] 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:8] 494882 494882 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:8] "SRS3883131" "SRS3883132" "SRS3883138" "SRS3883139" ...
## ..$ BioSample : chr [1:8] "SAMN10182830" "SAMN10182829" "SAMN10182823" "SAMN10182822" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "933DEF81DFC64DB4A639103B1E72624D" "5FE6EE77E7F800F6C6EBA3C0288A68A5" "92EC35C1FE7FDD892EC41E6DC2E6EFEF" "8D43ACFD52D5B57543D007EFCD152DDD" ...
## ..$ ReadHash : chr [1:8] "6A19F6D7640CA1BD3FE383E59275E87B" "4C7CE392A8DECF0D81B7EFFE6232AF10" "1AE6117C82EE9B0BD10EE9865AD1BE6B" "2E2CA2837DB809DB0E5478FA61B1C6A2" ...
## $ absent : chr(0)## SRP163900:IL15 versus IL15+IL21 in ex vivo:IL15;SRX4804441,SRX4804448,SRX4804455,SRX4804462,SRX4804469:IL15+IL21;SRX4804443,SRX4804450,SRX4804457,SRX4804464,SRX4804471;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 7 variables:
## ..$ SRR7971405: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971412: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971414: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971419: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971426: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971428: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971433: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 7 variables:
## ..$ SRR7971405: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971412: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971414: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971419: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971426: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971428: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971433: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 7 variables:
## ..$ SRR7971405: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971412: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971414: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971419: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971426: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971428: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971433: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 7 obs. of 7 variables:
## ..$ QC_summary : chr [1:7] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4)" ...
## ..$ SRX_accession: chr [1:7] "SRX4804441" "SRX4804448" "SRX4804450" "SRX4804455" ...
## ..$ SRS_accession: chr [1:7] "SRS3883131" "SRS3883138" "SRS3883140" "SRS3883145" ...
## ..$ SRP_accession: chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:7] "GSM3418205" "GSM3418212" "GSM3418214" "GSM3418219" ...
## ..$ GEO_series : chr [1:7] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 7 obs. of 52 variables:
## ..$ QC_summary : chr [1:7] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4)" ...
## ..$ SRX_accession : chr [1:7] "SRX4804441" "SRX4804448" "SRX4804450" "SRX4804455" ...
## ..$ SRS_accession : chr [1:7] "SRS3883131" "SRS3883138" "SRS3883140" "SRS3883145" ...
## ..$ SRP_accession : chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:7] "GSM3418205" "GSM3418212" "GSM3418214" "GSM3418219" ...
## ..$ GEO_series : chr [1:7] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:7] "GSM3418205" "GSM3418212" "GSM3418214" "GSM3418219" ...
## ..$ ReleaseDate : chr [1:7] "2018-10-08 18:32:27" "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" ...
## ..$ LoadDate : chr [1:7] "2018-10-05 17:39:18" "2018-10-05 17:42:41" "2018-10-05 17:42:59" "2018-10-05 17:41:10" ...
## ..$ spots : int [1:7] 16698270 21133448 21589341 16118899 21776546 19894344 22240028
## ..$ bases : int [1:7] 834913500 1056672400 1079467050 805944950 1088827300 994717200 1112001400
## ..$ spots_with_mates : int [1:7] 0 0 0 0 0 0 0
## ..$ avgLength : int [1:7] 50 50 50 50 50 50 50
## ..$ size_MB : int [1:7] 285 360 370 275 371 339 379
## ..$ AssemblyName : logi [1:7] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:7] "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971405" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971412" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971414" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971419/SRR7971419.1" ...
## ..$ LibraryName : logi [1:7] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:7] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:7] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:7] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:7] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:7] 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:7] 0 0 0 0 0 0 0
## ..$ Platform : chr [1:7] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:7] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:7] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:7] 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:7] 494882 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:7] "SRS3883131" "SRS3883138" "SRS3883140" "SRS3883145" ...
## ..$ BioSample : chr [1:7] "SAMN10182830" "SAMN10182823" "SAMN10182821" "SAMN10182816" ...
## ..$ SampleType : chr [1:7] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:7] 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:7] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:7] NA NA NA NA NA NA ...
## ..$ source : logi [1:7] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:7] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:7] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:7] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:7] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:7] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:7] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:7] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:7] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:7] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:7] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:7] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:7] "933DEF81DFC64DB4A639103B1E72624D" "92EC35C1FE7FDD892EC41E6DC2E6EFEF" "18AD04CD6E90CBC5906E736680D80632" "FA529DC8D7AFAE168E28B6663F961727" ...
## ..$ ReadHash : chr [1:7] "6A19F6D7640CA1BD3FE383E59275E87B" "1AE6117C82EE9B0BD10EE9865AD1BE6B" "A9DC81F3060CB0F44DE4E233DDFC5822" "A620D5F7410C2255D8E1ACE7F7B8DB42" ...
## $ absent : chr(0)## SRP163900:IL15+IL21 versus IL15+IL21+BNZ in ex vivo:IL15+IL21;SRX4804443,SRX4804450,SRX4804457,SRX4804464,SRX4804471:IL15+IL21+BNZ;SRX4804444,SRX4804451,SRX4804458,SRX4804465,SRX4804472;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 7 variables:
## ..$ SRR7971408: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971414: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971415: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971422: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971428: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971429: int [1:58302] 0 1 0 0 0 0 0 0 2 0 ...
## ..$ SRR7971436: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 7 variables:
## ..$ SRR7971408: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971414: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971415: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971422: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971428: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971429: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971436: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 7 variables:
## ..$ SRR7971408: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971414: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971415: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971422: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971428: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971429: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971436: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 7 obs. of 7 variables:
## ..$ QC_summary : chr [1:7] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4)" ...
## ..$ SRX_accession: chr [1:7] "SRX4804444" "SRX4804450" "SRX4804451" "SRX4804458" ...
## ..$ SRS_accession: chr [1:7] "SRS3883134" "SRS3883140" "SRS3883141" "SRS3883148" ...
## ..$ SRP_accession: chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:7] "GSM3418208" "GSM3418214" "GSM3418215" "GSM3418222" ...
## ..$ GEO_series : chr [1:7] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 7 obs. of 52 variables:
## ..$ QC_summary : chr [1:7] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4)" ...
## ..$ SRX_accession : chr [1:7] "SRX4804444" "SRX4804450" "SRX4804451" "SRX4804458" ...
## ..$ SRS_accession : chr [1:7] "SRS3883134" "SRS3883140" "SRS3883141" "SRS3883148" ...
## ..$ SRP_accession : chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:7] "GSM3418208" "GSM3418214" "GSM3418215" "GSM3418222" ...
## ..$ GEO_series : chr [1:7] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:7] "GSM3418208" "GSM3418214" "GSM3418215" "GSM3418222" ...
## ..$ ReleaseDate : chr [1:7] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" ...
## ..$ LoadDate : chr [1:7] "2018-10-05 17:42:45" "2018-10-05 17:42:59" "2018-10-05 17:43:07" "2018-10-05 17:41:18" ...
## ..$ spots : int [1:7] 19661548 21589341 26063162 15356672 19894344 23188591 23959497
## ..$ bases : int [1:7] 983077400 1079467050 1303158100 767833600 994717200 1159429550 1197974850
## ..$ spots_with_mates : int [1:7] 0 0 0 0 0 0 0
## ..$ avgLength : int [1:7] 50 50 50 50 50 50 50
## ..$ size_MB : int [1:7] 335 370 444 262 339 395 407
## ..$ AssemblyName : logi [1:7] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:7] "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971408" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971414" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971415" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971422/SRR7971422.1" ...
## ..$ LibraryName : logi [1:7] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:7] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:7] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:7] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:7] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:7] 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:7] 0 0 0 0 0 0 0
## ..$ Platform : chr [1:7] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:7] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:7] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:7] 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:7] 494882 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:7] "SRS3883134" "SRS3883140" "SRS3883141" "SRS3883148" ...
## ..$ BioSample : chr [1:7] "SAMN10182827" "SAMN10182821" "SAMN10182820" "SAMN10182813" ...
## ..$ SampleType : chr [1:7] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:7] 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:7] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:7] NA NA NA NA NA NA ...
## ..$ source : logi [1:7] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:7] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:7] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:7] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:7] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:7] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:7] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:7] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:7] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:7] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:7] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:7] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:7] "741C0570226F812DE513DDFF820BB45C" "18AD04CD6E90CBC5906E736680D80632" "5606EE3D61DD0E70E2B88B1265B24A55" "F5C0912D0404DAEA0BC2C29E83B4D826" ...
## ..$ ReadHash : chr [1:7] "C5E81A8B4C810BD215D9050F7E1D4FBB" "A9DC81F3060CB0F44DE4E233DDFC5822" "140FFAB316CFB32CD9652DF020498518" "DEF9FD2314AC6F3D933AF2345F1B83A5" ...
## $ absent : chr(0)## SRP163900:UN versus IL21 in ex vivo:UN;SRX4804447,SRX4804454,SRX4804461,SRX4804468,SRX4804475:IL21;SRX4804445,SRX4804452,SRX4804459,SRX4804466,SRX4804473;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR7971409: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971411: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971416: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971418: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971423: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971425: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971430: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971432: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971437: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971439: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR7971409: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971411: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971416: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971418: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971423: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971425: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971430: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971432: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971437: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971439: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR7971409: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971411: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971416: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971418: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971423: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971425: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971430: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971432: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971437: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971439: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "FAIL(4,6)" "FAIL(1,2,3,4,5,6,7)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession: chr [1:10] "SRX4804445" "SRX4804447" "SRX4804452" "SRX4804454" ...
## ..$ SRS_accession: chr [1:10] "SRS3883135" "SRS3883137" "SRS3883142" "SRS3883144" ...
## ..$ SRP_accession: chr [1:10] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:10] "GSM3418209" "GSM3418211" "GSM3418216" "GSM3418218" ...
## ..$ GEO_series : chr [1:10] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "FAIL(4,6)" "FAIL(1,2,3,4,5,6,7)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession : chr [1:10] "SRX4804445" "SRX4804447" "SRX4804452" "SRX4804454" ...
## ..$ SRS_accession : chr [1:10] "SRS3883135" "SRS3883137" "SRS3883142" "SRS3883144" ...
## ..$ SRP_accession : chr [1:10] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:10] "GSM3418209" "GSM3418211" "GSM3418216" "GSM3418218" ...
## ..$ GEO_series : chr [1:10] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM3418209" "GSM3418211" "GSM3418216" "GSM3418218" ...
## ..$ ReleaseDate : chr [1:10] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" ...
## ..$ LoadDate : chr [1:10] "2018-10-05 17:40:09" "2018-10-05 17:40:49" "2018-10-05 17:41:27" "2018-10-05 17:42:10" ...
## ..$ spots : int [1:10] 14896634 21139720 17311652 19838533 17910610 19404043 18459490 17862895 22023657 22338230
## ..$ bases : int [1:10] 744831700 1056986000 865582600 991926650 895530500 970202150 922974500 893144750 1101182850 1116911500
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 50 50 50 50 50 50 50 50 50 50
## ..$ size_MB : int [1:10] 254 360 295 338 306 329 314 304 375 381
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971409" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971411/SRR7971411.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971416/SRR7971416.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971418" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:10] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 494882 494882 494882 494882 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:10] "SRS3883135" "SRS3883137" "SRS3883142" "SRS3883144" ...
## ..$ BioSample : chr [1:10] "SAMN10182826" "SAMN10182824" "SAMN10182819" "SAMN10182817" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "2F9A28BE98FE8D685D1B8984D10E1538" "5A885C068A3E0EA8572E5A149C2E21E5" "79F1774959A4998C8C165A32F1F378A4" "0F420CD37A17545F4931051DB2780696" ...
## ..$ ReadHash : chr [1:10] "DDE1EA5FC79DDF80F3494BA96ABD1338" "14BCD07846B0101F53EEA56CB90CCACB" "9808B85FDA8ADBFFFFD99F476D87B46B" "8F85718181702F31869A2C8E7848E21E" ...
## $ absent : chr(0)## SRP163900:IL21 versus Il21+BNZ in ex vivo:IL21;SRX4804445,SRX4804452,SRX4804459,SRX4804466,SRX4804473:Il21+BNZ;SRX4804446,SRX4804453,SRX4804460,SRX4804467,SRX4804474;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR7971409: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971410: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971416: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971417: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971423: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971430: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971437: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971438: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR7971409: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971410: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971416: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971417: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971423: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971430: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971437: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971438: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR7971409: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971410: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971416: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971417: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971423: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971430: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971437: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971438: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "FAIL(4,6)" "FAIL(3,4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession: chr [1:8] "SRX4804445" "SRX4804446" "SRX4804452" "SRX4804453" ...
## ..$ SRS_accession: chr [1:8] "SRS3883135" "SRS3883136" "SRS3883142" "SRS3883143" ...
## ..$ SRP_accession: chr [1:8] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:8] "GSM3418209" "GSM3418210" "GSM3418216" "GSM3418217" ...
## ..$ GEO_series : chr [1:8] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "FAIL(4,6)" "FAIL(3,4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession : chr [1:8] "SRX4804445" "SRX4804446" "SRX4804452" "SRX4804453" ...
## ..$ SRS_accession : chr [1:8] "SRS3883135" "SRS3883136" "SRS3883142" "SRS3883143" ...
## ..$ SRP_accession : chr [1:8] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:8] "GSM3418209" "GSM3418210" "GSM3418216" "GSM3418217" ...
## ..$ GEO_series : chr [1:8] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM3418209" "GSM3418210" "GSM3418216" "GSM3418217" ...
## ..$ ReleaseDate : chr [1:8] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" ...
## ..$ LoadDate : chr [1:8] "2018-10-05 17:40:09" "2018-10-05 17:41:36" "2018-10-05 17:41:27" "2018-10-05 17:42:57" ...
## ..$ spots : int [1:8] 14896634 19310656 17311652 22867849 17910610 18459490 22023657 21418392
## ..$ bases : int [1:8] 744831700 965532800 865582600 1143392450 895530500 922974500 1101182850 1070919600
## ..$ spots_with_mates : int [1:8] 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:8] 50 50 50 50 50 50 50 50
## ..$ size_MB : int [1:8] 254 332 295 410 306 314 375 366
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971409" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971410/SRR7971410.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971416/SRR7971416.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971417" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:8] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:8] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:8] 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:8] 494882 494882 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:8] "SRS3883135" "SRS3883136" "SRS3883142" "SRS3883143" ...
## ..$ BioSample : chr [1:8] "SAMN10182826" "SAMN10182825" "SAMN10182819" "SAMN10182818" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "2F9A28BE98FE8D685D1B8984D10E1538" "F9725BE70F3B4D7A63666F27040A1F17" "79F1774959A4998C8C165A32F1F378A4" "19DB62ACA2C873C210A412FA5DB2D8A0" ...
## ..$ ReadHash : chr [1:8] "DDE1EA5FC79DDF80F3494BA96ABD1338" "9310BD24C36AACCF2CD003CE253E04A8" "9808B85FDA8ADBFFFFD99F476D87B46B" "A1BFC4F35547112A6164AF9556DEAFF0" ...
## $ absent : chr(0)## SRP163900:UN versus IL15 in in vitro:UN;SRX4804485,SRX4804495,SRX4804505,SRX4804515,SRX4804519,SRX4804523,SRX4804527:IL15;SRX4804476,SRX4804486,SRX4804496,SRX4804506;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR7971440: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971450: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971459: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971460: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971469: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971470: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971479: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971483: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971487: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971491: int [1:58302] 0 0 0 0 0 0 0 0 0 2 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR7971440: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971450: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971459: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971460: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971469: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971470: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971479: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971483: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971487: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971491: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR7971440: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971450: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971459: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971460: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971469: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971470: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971479: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971483: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971487: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971491: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "WARN(4,5,6,7)" "WARN(3,4,5,6,7,8)" "WARN(3,4,5,6,7,8)" "WARN(4,6)" ...
## ..$ SRX_accession: chr [1:10] "SRX4804476" "SRX4804486" "SRX4804495" "SRX4804496" ...
## ..$ SRS_accession: chr [1:10] "SRS3883166" "SRS3883177" "SRS3883185" "SRS3883186" ...
## ..$ SRP_accession: chr [1:10] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:10] "GSM3418240" "GSM3418250" "GSM3418259" "GSM3418260" ...
## ..$ GEO_series : chr [1:10] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "WARN(4,5,6,7)" "WARN(3,4,5,6,7,8)" "WARN(3,4,5,6,7,8)" "WARN(4,6)" ...
## ..$ SRX_accession : chr [1:10] "SRX4804476" "SRX4804486" "SRX4804495" "SRX4804496" ...
## ..$ SRS_accession : chr [1:10] "SRS3883166" "SRS3883177" "SRS3883185" "SRS3883186" ...
## ..$ SRP_accession : chr [1:10] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:10] "GSM3418240" "GSM3418250" "GSM3418259" "GSM3418260" ...
## ..$ GEO_series : chr [1:10] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM3418240" "GSM3418250" "GSM3418259" "GSM3418260" ...
## ..$ ReleaseDate : chr [1:10] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:29" "2018-10-08 18:32:29" ...
## ..$ LoadDate : chr [1:10] "2018-10-05 17:41:36" "2018-10-05 17:40:50" "2018-10-05 17:41:04" "2018-10-05 17:43:00" ...
## ..$ spots : int [1:10] 17330660 14303234 13100308 24324960 15955087 18291054 20140065 17221463 18470007 22802093
## ..$ bases : int [1:10] 866533000 715161700 655015400 1216248000 797754350 914552700 1007003250 861073150 923500350 1140104650
## ..$ spots_with_mates : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:10] 50 50 50 50 50 50 50 50 50 50
## ..$ size_MB : int [1:10] 327 286 248 479 305 342 360 312 334 415
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971440/SRR7971440.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971450/SRR7971450.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971459/SRR7971459.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971460" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:10] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:10] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:10] 3 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:10] 494882 494882 494882 494882 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:10] "SRS3883166" "SRS3883177" "SRS3883185" "SRS3883186" ...
## ..$ BioSample : chr [1:10] "SAMN10182765" "SAMN10182755" "SAMN10182833" "SAMN10182832" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "B2DCD285BAC30F9AFC566EDB8FE5AF54" "00BB13F9E68CC0F2A458BA3A0AC98DCB" "D5467593BFD1704C2D5F7851F8A487E7" "8FCA3F2C68AFBB0B4FCC6B1B5EDF8895" ...
## ..$ ReadHash : chr [1:10] "B8109DDAAD3E08B632F21DDAAE74A8B0" "866F62A3FA804F049A9FA1533C088DF5" "AC37E9B1A1D38AE6F5F8BBCA661805C6" "A717E8F52D0873A036A33B0EB63A7262" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP163900:IL15 versus IL15+BNZ in in vitro:IL15;SRX4804476,SRX4804486,SRX4804496,SRX4804506:IL15+BNZ;SRX4804477,SRX4804487,SRX4804497,SRX4804507;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 7 variables:
## ..$ SRR7971440: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971441: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971450: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971460: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971461: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971470: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971471: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 7 variables:
## ..$ SRR7971440: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971441: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971450: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971460: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971461: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971470: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971471: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 7 variables:
## ..$ SRR7971440: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971441: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971450: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971460: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971461: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971470: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971471: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 7 obs. of 7 variables:
## ..$ QC_summary : chr [1:7] "WARN(4,5,6,7)" "WARN(3,4,5,6,7)" "WARN(3,4,5,6,7,8)" "WARN(4,6)" ...
## ..$ SRX_accession: chr [1:7] "SRX4804476" "SRX4804477" "SRX4804486" "SRX4804496" ...
## ..$ SRS_accession: chr [1:7] "SRS3883166" "SRS3883167" "SRS3883177" "SRS3883186" ...
## ..$ SRP_accession: chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:7] "GSM3418240" "GSM3418241" "GSM3418250" "GSM3418260" ...
## ..$ GEO_series : chr [1:7] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 7 obs. of 52 variables:
## ..$ QC_summary : chr [1:7] "WARN(4,5,6,7)" "WARN(3,4,5,6,7)" "WARN(3,4,5,6,7,8)" "WARN(4,6)" ...
## ..$ SRX_accession : chr [1:7] "SRX4804476" "SRX4804477" "SRX4804486" "SRX4804496" ...
## ..$ SRS_accession : chr [1:7] "SRS3883166" "SRS3883167" "SRS3883177" "SRS3883186" ...
## ..$ SRP_accession : chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:7] "GSM3418240" "GSM3418241" "GSM3418250" "GSM3418260" ...
## ..$ GEO_series : chr [1:7] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:7] "GSM3418240" "GSM3418241" "GSM3418250" "GSM3418260" ...
## ..$ ReleaseDate : chr [1:7] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:29" ...
## ..$ LoadDate : chr [1:7] "2018-10-05 17:41:36" "2018-10-05 17:42:46" "2018-10-05 17:40:50" "2018-10-05 17:43:00" ...
## ..$ spots : int [1:7] 17330660 19180526 14303234 24324960 20078779 18291054 19750631
## ..$ bases : int [1:7] 866533000 959026300 715161700 1216248000 1003938950 914552700 987531550
## ..$ spots_with_mates : int [1:7] 0 0 0 0 0 0 0
## ..$ avgLength : int [1:7] 50 50 50 50 50 50 50
## ..$ size_MB : int [1:7] 327 352 286 479 384 342 353
## ..$ AssemblyName : logi [1:7] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:7] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971440/SRR7971440.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971441" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971450/SRR7971450.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971460" ...
## ..$ LibraryName : logi [1:7] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:7] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:7] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:7] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:7] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:7] 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:7] 0 0 0 0 0 0 0
## ..$ Platform : chr [1:7] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:7] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:7] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:7] 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:7] 494882 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:7] "SRS3883166" "SRS3883167" "SRS3883177" "SRS3883186" ...
## ..$ BioSample : chr [1:7] "SAMN10182765" "SAMN10182764" "SAMN10182755" "SAMN10182832" ...
## ..$ SampleType : chr [1:7] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:7] 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:7] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:7] NA NA NA NA NA NA ...
## ..$ source : logi [1:7] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:7] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:7] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:7] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:7] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:7] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:7] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:7] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:7] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:7] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:7] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:7] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:7] "B2DCD285BAC30F9AFC566EDB8FE5AF54" "6EBE305AF9573EE88F19225FABDC8751" "00BB13F9E68CC0F2A458BA3A0AC98DCB" "8FCA3F2C68AFBB0B4FCC6B1B5EDF8895" ...
## ..$ ReadHash : chr [1:7] "B8109DDAAD3E08B632F21DDAAE74A8B0" "630613D7BBB677297C8D241A68C3A599" "866F62A3FA804F049A9FA1533C088DF5" "A717E8F52D0873A036A33B0EB63A7262" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP163900:IL15 versus IL15+IL21 in in vitro:IL15;SRX4804476,SRX4804486,SRX4804496,SRX4804506:Il15+IL21;SRX4804479,SRX4804489,SRX4804499,SRX4804509;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR7971440: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971443: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971450: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971453: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971460: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971463: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971470: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971473: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR7971440: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971443: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971450: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971453: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971460: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971463: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971470: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971473: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR7971440: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971443: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971450: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971453: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971460: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971463: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971470: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971473: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "WARN(4,5,6,7)" "WARN(4,5,6)" "WARN(3,4,5,6,7,8)" "WARN(3,4,5,6,7,8)" ...
## ..$ SRX_accession: chr [1:8] "SRX4804476" "SRX4804479" "SRX4804486" "SRX4804489" ...
## ..$ SRS_accession: chr [1:8] "SRS3883166" "SRS3883169" "SRS3883177" "SRS3883179" ...
## ..$ SRP_accession: chr [1:8] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:8] "GSM3418240" "GSM3418243" "GSM3418250" "GSM3418253" ...
## ..$ GEO_series : chr [1:8] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "WARN(4,5,6,7)" "WARN(4,5,6)" "WARN(3,4,5,6,7,8)" "WARN(3,4,5,6,7,8)" ...
## ..$ SRX_accession : chr [1:8] "SRX4804476" "SRX4804479" "SRX4804486" "SRX4804489" ...
## ..$ SRS_accession : chr [1:8] "SRS3883166" "SRS3883169" "SRS3883177" "SRS3883179" ...
## ..$ SRP_accession : chr [1:8] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:8] "GSM3418240" "GSM3418243" "GSM3418250" "GSM3418253" ...
## ..$ GEO_series : chr [1:8] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM3418240" "GSM3418243" "GSM3418250" "GSM3418253" ...
## ..$ ReleaseDate : chr [1:8] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" ...
## ..$ LoadDate : chr [1:8] "2018-10-05 17:41:36" "2018-10-05 17:43:31" "2018-10-05 17:40:50" "2018-10-05 17:42:18" ...
## ..$ spots : int [1:8] 17330660 18949926 14303234 17846585 24324960 21991469 18291054 18842862
## ..$ bases : int [1:8] 866533000 947496300 715161700 892329250 1216248000 1099573450 914552700 942143100
## ..$ spots_with_mates : int [1:8] 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:8] 50 50 50 50 50 50 50 50
## ..$ size_MB : int [1:8] 327 348 286 338 479 421 342 337
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971440/SRR7971440.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971443" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971450/SRR7971450.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971453" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:8] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:8] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:8] 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:8] 494882 494882 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:8] "SRS3883166" "SRS3883169" "SRS3883177" "SRS3883179" ...
## ..$ BioSample : chr [1:8] "SAMN10182765" "SAMN10182762" "SAMN10182755" "SAMN10182752" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "B2DCD285BAC30F9AFC566EDB8FE5AF54" "B443F450A468DF67817D89F122122F67" "00BB13F9E68CC0F2A458BA3A0AC98DCB" "DFBC0434234BB46E6056B441FBAC7042" ...
## ..$ ReadHash : chr [1:8] "B8109DDAAD3E08B632F21DDAAE74A8B0" "22EF3357B85FD0ACA1DD2E4EDEB9FD88" "866F62A3FA804F049A9FA1533C088DF5" "C1D98422A997EB2AFB6F0511E63019BB" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP163900:IL15+IL21 versus IL15+IL21+BNZ in in vitro:IL15+IL21;SRX4804479,SRX4804489,SRX4804499,SRX4804509:IL15+IL21+BNZ;SRX4804480,SRX4804490,SRX4804500,SRX4804510;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 7 variables:
## ..$ SRR7971443: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971444: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971453: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971463: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971464: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971473: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR7971474: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 7 variables:
## ..$ SRR7971443: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971444: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971453: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971463: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971464: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971473: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971474: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 7 variables:
## ..$ SRR7971443: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971444: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971453: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971463: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971464: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971473: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971474: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 7 obs. of 7 variables:
## ..$ QC_summary : chr [1:7] "WARN(4,5,6)" "WARN(3,4,5,6,7,8)" "WARN(3,4,5,6,7,8)" "WARN(3,4,6)" ...
## ..$ SRX_accession: chr [1:7] "SRX4804479" "SRX4804480" "SRX4804489" "SRX4804499" ...
## ..$ SRS_accession: chr [1:7] "SRS3883169" "SRS3883170" "SRS3883179" "SRS3883189" ...
## ..$ SRP_accession: chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:7] "GSM3418243" "GSM3418244" "GSM3418253" "GSM3418263" ...
## ..$ GEO_series : chr [1:7] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 7 obs. of 52 variables:
## ..$ QC_summary : chr [1:7] "WARN(4,5,6)" "WARN(3,4,5,6,7,8)" "WARN(3,4,5,6,7,8)" "WARN(3,4,6)" ...
## ..$ SRX_accession : chr [1:7] "SRX4804479" "SRX4804480" "SRX4804489" "SRX4804499" ...
## ..$ SRS_accession : chr [1:7] "SRS3883169" "SRS3883170" "SRS3883179" "SRS3883189" ...
## ..$ SRP_accession : chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:7] "GSM3418243" "GSM3418244" "GSM3418253" "GSM3418263" ...
## ..$ GEO_series : chr [1:7] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:7] "GSM3418243" "GSM3418244" "GSM3418253" "GSM3418263" ...
## ..$ ReleaseDate : chr [1:7] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:29" ...
## ..$ LoadDate : chr [1:7] "2018-10-05 17:43:31" "2018-10-05 17:42:26" "2018-10-05 17:42:18" "2018-10-05 17:43:24" ...
## ..$ spots : int [1:7] 18949926 18000635 17846585 21991469 22959319 18842862 17636204
## ..$ bases : int [1:7] 947496300 900031750 892329250 1099573450 1147965950 942143100 881810200
## ..$ spots_with_mates : int [1:7] 0 0 0 0 0 0 0
## ..$ avgLength : int [1:7] 50 50 50 50 50 50 50
## ..$ size_MB : int [1:7] 348 329 338 421 438 337 315
## ..$ AssemblyName : logi [1:7] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:7] "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971443" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971444" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971453" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971463" ...
## ..$ LibraryName : logi [1:7] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:7] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:7] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:7] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:7] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:7] 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:7] 0 0 0 0 0 0 0
## ..$ Platform : chr [1:7] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:7] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:7] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:7] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:7] 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:7] 494882 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:7] "SRS3883169" "SRS3883170" "SRS3883179" "SRS3883189" ...
## ..$ BioSample : chr [1:7] "SAMN10182762" "SAMN10182761" "SAMN10182752" "SAMN10182802" ...
## ..$ SampleType : chr [1:7] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:7] 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:7] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:7] NA NA NA NA NA NA ...
## ..$ source : logi [1:7] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:7] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:7] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:7] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:7] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:7] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:7] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:7] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:7] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:7] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:7] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:7] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:7] "B443F450A468DF67817D89F122122F67" "8573A75417218FE11E6A99CAD791A277" "DFBC0434234BB46E6056B441FBAC7042" "16363EB5A844F8EA1CF38EEE02CC6523" ...
## ..$ ReadHash : chr [1:7] "22EF3357B85FD0ACA1DD2E4EDEB9FD88" "9FFB45CCA30A68F8002D1FC9913C9759" "C1D98422A997EB2AFB6F0511E63019BB" "D076FFCE966B0856013EEDE2EF64BFAB" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP163900:UN versus IL21 in in vitro:UN;SRX4804485,SRX4804495,SRX4804505,SRX4804515,SRX4804519,SRX4804523,SRX4804527:IL21;SRX4804482,SRX4804492,SRX4804502,SRX4804512,SRX4804516,SRX4804520,SRX4804524;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 13 variables:
## ..$ SRR7971446: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971456: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971459: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971466: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971469: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971476: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971479: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971480: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971483: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971484: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971487: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971488: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971491: int [1:58302] 0 0 0 0 0 0 0 0 0 2 ...
## $ TxCounts :'data.frame': 180869 obs. of 13 variables:
## ..$ SRR7971446: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971456: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971459: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971466: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971469: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971476: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971479: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971480: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971483: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971484: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971487: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971488: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971491: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 13 variables:
## ..$ SRR7971446: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971456: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971459: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971466: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971469: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971476: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971479: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971480: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971483: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971484: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971487: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971488: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971491: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 13 obs. of 7 variables:
## ..$ QC_summary : chr [1:13] "WARN(4,5,6,7)" "WARN(3,4,6,8)" "WARN(3,4,5,6,7,8)" "WARN(3,4,6)" ...
## ..$ SRX_accession: chr [1:13] "SRX4804482" "SRX4804492" "SRX4804495" "SRX4804502" ...
## ..$ SRS_accession: chr [1:13] "SRS3883172" "SRS3883182" "SRS3883185" "SRS3883192" ...
## ..$ SRP_accession: chr [1:13] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:13] "GSM3418246" "GSM3418256" "GSM3418259" "GSM3418266" ...
## ..$ GEO_series : chr [1:13] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:13] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 13 obs. of 52 variables:
## ..$ QC_summary : chr [1:13] "WARN(4,5,6,7)" "WARN(3,4,6,8)" "WARN(3,4,5,6,7,8)" "WARN(3,4,6)" ...
## ..$ SRX_accession : chr [1:13] "SRX4804482" "SRX4804492" "SRX4804495" "SRX4804502" ...
## ..$ SRS_accession : chr [1:13] "SRS3883172" "SRS3883182" "SRS3883185" "SRS3883192" ...
## ..$ SRP_accession : chr [1:13] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:13] "GSM3418246" "GSM3418256" "GSM3418259" "GSM3418266" ...
## ..$ GEO_series : chr [1:13] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:13] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:13] "GSM3418246" "GSM3418256" "GSM3418259" "GSM3418266" ...
## ..$ ReleaseDate : chr [1:13] "2018-10-08 18:32:28" "2018-10-08 18:32:29" "2018-10-08 18:32:29" "2018-10-08 18:32:29" ...
## ..$ LoadDate : chr [1:13] "2018-10-05 17:41:33" "2018-10-05 17:44:33" "2018-10-05 17:41:04" "2018-10-05 17:44:43" ...
## ..$ spots : int [1:13] 15094533 24757018 13100308 25589765 15955087 17158036 20140065 23819188 17221463 16568164 ...
## ..$ bases : int [1:13] 754726650 1237850900 655015400 1279488250 797754350 857901800 1007003250 1190959400 861073150 828408200 ...
## ..$ spots_with_mates : int [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:13] 50 50 50 50 50 50 50 50 50 50 ...
## ..$ size_MB : int [1:13] 277 471 248 489 305 306 360 432 312 299 ...
## ..$ AssemblyName : logi [1:13] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:13] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971446/SRR7971446.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971456" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971459/SRR7971459.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971466/SRR7971466.1" ...
## ..$ LibraryName : logi [1:13] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:13] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:13] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:13] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:13] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:13] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:13] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:13] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:13] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:13] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:13] 494882 494882 494882 494882 494882 494882 494882 494882 494882 494882 ...
## ..$ Sample : chr [1:13] "SRS3883172" "SRS3883182" "SRS3883185" "SRS3883192" ...
## ..$ BioSample : chr [1:13] "SAMN10182759" "SAMN10182836" "SAMN10182833" "SAMN10182799" ...
## ..$ SampleType : chr [1:13] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:13] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:13] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:13] NA NA NA NA NA NA ...
## ..$ source : logi [1:13] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:13] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:13] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:13] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:13] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:13] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:13] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:13] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:13] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:13] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:13] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:13] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:13] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:13] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:13] "7A391ECA7C2C61E88097F5792BF5C6FF" "363F123604038BEBA836C7056ABAC460" "D5467593BFD1704C2D5F7851F8A487E7" "5713EDBBB2B4B6A8BEE01E06C01E8AC3" ...
## ..$ ReadHash : chr [1:13] "E55A81F05509136B96B454AF73CA75F3" "46EED80BEED1EF92933479B0A8CF0B2C" "AC37E9B1A1D38AE6F5F8BBCA661805C6" "FF7455E9F965BE64247E2CE433642300" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 14 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP163900:IL21 versus Il21+BNZ in in vitro:IL21;SRX4804482,SRX4804492,SRX4804502,SRX4804512,SRX4804516,SRX4804520,SRX4804524:IL21+BNZ;SRX4804483,SRX4804493,SRX4804503,SRX4804513,SRX4804517,SRX4804521,SRX4804525;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 12 variables:
## ..$ SRR7971446: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971447: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971456: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971457: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971466: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971467: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971476: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971477: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971480: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971484: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971485: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971488: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 12 variables:
## ..$ SRR7971446: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971447: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971456: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971457: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971466: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971467: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971476: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971477: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971480: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971484: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971485: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971488: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 12 variables:
## ..$ SRR7971446: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971447: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971456: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971457: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971466: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971467: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971476: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971477: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971480: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971484: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971485: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971488: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 12 obs. of 7 variables:
## ..$ QC_summary : chr [1:12] "WARN(4,5,6,7)" "WARN(3,4,5,6,7,8)" "WARN(3,4,6,8)" "WARN(3,4,5,6,8)" ...
## ..$ SRX_accession: chr [1:12] "SRX4804482" "SRX4804483" "SRX4804492" "SRX4804493" ...
## ..$ SRS_accession: chr [1:12] "SRS3883172" "SRS3883173" "SRS3883182" "SRS3883183" ...
## ..$ SRP_accession: chr [1:12] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:12] "GSM3418246" "GSM3418247" "GSM3418256" "GSM3418257" ...
## ..$ GEO_series : chr [1:12] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:12] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 12 obs. of 52 variables:
## ..$ QC_summary : chr [1:12] "WARN(4,5,6,7)" "WARN(3,4,5,6,7,8)" "WARN(3,4,6,8)" "WARN(3,4,5,6,8)" ...
## ..$ SRX_accession : chr [1:12] "SRX4804482" "SRX4804483" "SRX4804492" "SRX4804493" ...
## ..$ SRS_accession : chr [1:12] "SRS3883172" "SRS3883173" "SRS3883182" "SRS3883183" ...
## ..$ SRP_accession : chr [1:12] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:12] "GSM3418246" "GSM3418247" "GSM3418256" "GSM3418257" ...
## ..$ GEO_series : chr [1:12] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:12] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:12] "GSM3418246" "GSM3418247" "GSM3418256" "GSM3418257" ...
## ..$ ReleaseDate : chr [1:12] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:29" "2018-10-08 18:32:29" ...
## ..$ LoadDate : chr [1:12] "2018-10-05 17:41:33" "2018-10-05 17:43:06" "2018-10-05 17:44:33" "2018-10-05 17:42:24" ...
## ..$ spots : int [1:12] 15094533 17224819 24757018 18429017 25589765 17693461 17158036 16390839 23819188 16568164 ...
## ..$ bases : int [1:12] 754726650 861240950 1237850900 921450850 1279488250 884673050 857901800 819541950 1190959400 828408200 ...
## ..$ spots_with_mates : int [1:12] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:12] 50 50 50 50 50 50 50 50 50 50 ...
## ..$ size_MB : int [1:12] 277 317 471 351 489 338 306 294 432 299 ...
## ..$ AssemblyName : logi [1:12] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:12] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971446/SRR7971446.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971447" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971456" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971457" ...
## ..$ LibraryName : logi [1:12] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:12] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:12] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:12] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:12] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:12] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:12] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:12] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:12] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:12] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:12] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:12] 494882 494882 494882 494882 494882 494882 494882 494882 494882 494882 ...
## ..$ Sample : chr [1:12] "SRS3883172" "SRS3883173" "SRS3883182" "SRS3883183" ...
## ..$ BioSample : chr [1:12] "SAMN10182759" "SAMN10182758" "SAMN10182836" "SAMN10182835" ...
## ..$ SampleType : chr [1:12] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:12] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:12] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:12] NA NA NA NA NA NA ...
## ..$ source : logi [1:12] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:12] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:12] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:12] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:12] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:12] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:12] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:12] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:12] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:12] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:12] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:12] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:12] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:12] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:12] "7A391ECA7C2C61E88097F5792BF5C6FF" "406D4C0B78D90D149DFA002C320D977B" "363F123604038BEBA836C7056ABAC460" "74E909EB63250433C45EB2AAAD952452" ...
## ..$ ReadHash : chr [1:12] "E55A81F05509136B96B454AF73CA75F3" "9654BBFAE7B42A0B797D711AA9EE2278" "46EED80BEED1EF92933479B0A8CF0B2C" "E47CF05AB717B8818EC608AD0FF7B1A1" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 15 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP163900:IL21 versus IL21+CP in in vitro:IL21;SRX4804482,SRX4804492,SRX4804502,SRX4804512,SRX4804516,SRX4804520,SRX4804524:IL21+CP;SRX4804484,SRX4804494,SRX4804504,SRX4804514,SRX4804518,SRX4804522,SRX4804526;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 13 variables:
## ..$ SRR7971446: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971448: int [1:58302] 0 0 0 2 0 0 0 0 0 0 ...
## ..$ SRR7971456: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971458: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971466: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971468: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971476: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971480: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971482: int [1:58302] 0 0 0 0 0 0 0 0 0 2 ...
## ..$ SRR7971484: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971486: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971488: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971490: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 13 variables:
## ..$ SRR7971446: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971448: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971456: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971458: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971466: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971468: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971476: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971480: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971482: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971484: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971486: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971488: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971490: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 13 variables:
## ..$ SRR7971446: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971448: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971456: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971458: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971466: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971468: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971476: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971480: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971482: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971484: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971486: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971488: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971490: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 13 obs. of 7 variables:
## ..$ QC_summary : chr [1:13] "WARN(4,5,6,7)" "WARN(3,4,5,6,7)" "WARN(3,4,6,8)" "WARN(3,4,6,8)" ...
## ..$ SRX_accession: chr [1:13] "SRX4804482" "SRX4804484" "SRX4804492" "SRX4804494" ...
## ..$ SRS_accession: chr [1:13] "SRS3883172" "SRS3883174" "SRS3883182" "SRS3883184" ...
## ..$ SRP_accession: chr [1:13] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:13] "GSM3418246" "GSM3418248" "GSM3418256" "GSM3418258" ...
## ..$ GEO_series : chr [1:13] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:13] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 13 obs. of 52 variables:
## ..$ QC_summary : chr [1:13] "WARN(4,5,6,7)" "WARN(3,4,5,6,7)" "WARN(3,4,6,8)" "WARN(3,4,6,8)" ...
## ..$ SRX_accession : chr [1:13] "SRX4804482" "SRX4804484" "SRX4804492" "SRX4804494" ...
## ..$ SRS_accession : chr [1:13] "SRS3883172" "SRS3883174" "SRS3883182" "SRS3883184" ...
## ..$ SRP_accession : chr [1:13] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:13] "GSM3418246" "GSM3418248" "GSM3418256" "GSM3418258" ...
## ..$ GEO_series : chr [1:13] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:13] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:13] "GSM3418246" "GSM3418248" "GSM3418256" "GSM3418258" ...
## ..$ ReleaseDate : chr [1:13] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:29" "2018-10-08 18:32:29" ...
## ..$ LoadDate : chr [1:13] "2018-10-05 17:41:33" "2018-10-05 17:41:05" "2018-10-05 17:44:33" "2018-10-05 17:44:49" ...
## ..$ spots : int [1:13] 15094533 18149147 24757018 27264240 25589765 24850483 17158036 23819188 21523264 16568164 ...
## ..$ bases : int [1:13] 754726650 907457350 1237850900 1363212000 1279488250 1242524150 857901800 1190959400 1076163200 828408200 ...
## ..$ spots_with_mates : int [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:13] 50 50 50 50 50 50 50 50 50 50 ...
## ..$ size_MB : int [1:13] 277 331 471 518 489 475 306 432 389 299 ...
## ..$ AssemblyName : logi [1:13] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:13] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971446/SRR7971446.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971448/SRR7971448.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971456" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971458/SRR7971458.1" ...
## ..$ LibraryName : logi [1:13] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:13] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:13] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:13] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:13] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:13] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:13] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:13] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:13] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:13] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:13] 494882 494882 494882 494882 494882 494882 494882 494882 494882 494882 ...
## ..$ Sample : chr [1:13] "SRS3883172" "SRS3883174" "SRS3883182" "SRS3883184" ...
## ..$ BioSample : chr [1:13] "SAMN10182759" "SAMN10182757" "SAMN10182836" "SAMN10182834" ...
## ..$ SampleType : chr [1:13] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:13] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:13] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:13] NA NA NA NA NA NA ...
## ..$ source : logi [1:13] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:13] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:13] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:13] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:13] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:13] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:13] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:13] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:13] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:13] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:13] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:13] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:13] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:13] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:13] "7A391ECA7C2C61E88097F5792BF5C6FF" "A809B6B82703D9D2DA60A532E446D0F7" "363F123604038BEBA836C7056ABAC460" "408F39ED5E98544FB1A659460F7A61EA" ...
## ..$ ReadHash : chr [1:13] "E55A81F05509136B96B454AF73CA75F3" "BC0DDBA3DB1F61F48C099341B33D16BC" "46EED80BEED1EF92933479B0A8CF0B2C" "566C4D9FE57CB722D6AC58701FE86F2A" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 9 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP163900:IL15 versus Il15+CP in in vitro:IL15;SRX4804476,SRX4804486,SRX4804496,SRX4804506:IL15+CP;SRX4804478,SRX4804488,SRX4804498,SRX4804508;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR7971440: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971450: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971460: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971462: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR7971470: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971472: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR7971440: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971450: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971460: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971462: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971470: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971472: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR7971440: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971450: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971460: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971462: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971470: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971472: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(4,5,6,7)" "WARN(3,4,5,6,7,8)" "WARN(4,6)" "WARN(4,5,6)" ...
## ..$ SRX_accession: chr [1:6] "SRX4804476" "SRX4804486" "SRX4804496" "SRX4804498" ...
## ..$ SRS_accession: chr [1:6] "SRS3883166" "SRS3883177" "SRS3883186" "SRS3883188" ...
## ..$ SRP_accession: chr [1:6] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:6] "GSM3418240" "GSM3418250" "GSM3418260" "GSM3418262" ...
## ..$ GEO_series : chr [1:6] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(4,5,6,7)" "WARN(3,4,5,6,7,8)" "WARN(4,6)" "WARN(4,5,6)" ...
## ..$ SRX_accession : chr [1:6] "SRX4804476" "SRX4804486" "SRX4804496" "SRX4804498" ...
## ..$ SRS_accession : chr [1:6] "SRS3883166" "SRS3883177" "SRS3883186" "SRS3883188" ...
## ..$ SRP_accession : chr [1:6] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:6] "GSM3418240" "GSM3418250" "GSM3418260" "GSM3418262" ...
## ..$ GEO_series : chr [1:6] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM3418240" "GSM3418250" "GSM3418260" "GSM3418262" ...
## ..$ ReleaseDate : chr [1:6] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:29" "2018-10-08 18:32:29" ...
## ..$ LoadDate : chr [1:6] "2018-10-05 17:41:36" "2018-10-05 17:40:50" "2018-10-05 17:43:00" "2018-10-05 17:42:49" ...
## ..$ spots : int [1:6] 17330660 14303234 24324960 21224458 18291054 15565571
## ..$ bases : int [1:6] 866533000 715161700 1216248000 1061222900 914552700 778278550
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 50 50 50 50 50 50
## ..$ size_MB : int [1:6] 327 286 479 404 342 278
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971440/SRR7971440.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR7971450/SRR7971450.1" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971460" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971462" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:6] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:6] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:6] "SRS3883166" "SRS3883177" "SRS3883186" "SRS3883188" ...
## ..$ BioSample : chr [1:6] "SAMN10182765" "SAMN10182755" "SAMN10182832" "SAMN10182803" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "B2DCD285BAC30F9AFC566EDB8FE5AF54" "00BB13F9E68CC0F2A458BA3A0AC98DCB" "8FCA3F2C68AFBB0B4FCC6B1B5EDF8895" "26226E00A9498D733F17CA01646C3975" ...
## ..$ ReadHash : chr [1:6] "B8109DDAAD3E08B632F21DDAAE74A8B0" "866F62A3FA804F049A9FA1533C088DF5" "A717E8F52D0873A036A33B0EB63A7262" "F1F5799808383EC72314313435573B45" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP163900:IL15+IL21 versus IL15+IL21+CP in in vitro:IL15+IL21;SRX4804479,SRX4804489,SRX4804499,SRX4804509:IL15+IL21+CP;SRX4804481,SRX4804491,SRX4804501,SRX4804511;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR7971443: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971445: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971453: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971463: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971473: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR7971475: int [1:58302] 0 0 0 1 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR7971443: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971445: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971453: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971463: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971473: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7971475: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR7971443: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971445: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971453: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971463: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971473: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR7971475: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(4,5,6)" "WARN(4,5,6,7)" "WARN(3,4,5,6,7,8)" "WARN(3,4,6)" ...
## ..$ SRX_accession: chr [1:6] "SRX4804479" "SRX4804481" "SRX4804489" "SRX4804499" ...
## ..$ SRS_accession: chr [1:6] "SRS3883169" "SRS3883171" "SRS3883179" "SRS3883189" ...
## ..$ SRP_accession: chr [1:6] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:6] "GSM3418243" "GSM3418245" "GSM3418253" "GSM3418263" ...
## ..$ GEO_series : chr [1:6] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(4,5,6)" "WARN(4,5,6,7)" "WARN(3,4,5,6,7,8)" "WARN(3,4,6)" ...
## ..$ SRX_accession : chr [1:6] "SRX4804479" "SRX4804481" "SRX4804489" "SRX4804499" ...
## ..$ SRS_accession : chr [1:6] "SRS3883169" "SRS3883171" "SRS3883179" "SRS3883189" ...
## ..$ SRP_accession : chr [1:6] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ Sample_name : chr [1:6] "GSM3418243" "GSM3418245" "GSM3418253" "GSM3418263" ...
## ..$ GEO_series : chr [1:6] "GSE120904" "GSE120904" "GSE120904" "GSE120904" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM3418243" "GSM3418245" "GSM3418253" "GSM3418263" ...
## ..$ ReleaseDate : chr [1:6] "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:28" "2018-10-08 18:32:29" ...
## ..$ LoadDate : chr [1:6] "2018-10-05 17:43:31" "2018-10-05 17:42:12" "2018-10-05 17:42:18" "2018-10-05 17:43:24" ...
## ..$ spots : int [1:6] 18949926 17080041 17846585 21991469 18842862 21920221
## ..$ bases : int [1:6] 947496300 854002050 892329250 1099573450 942143100 1096011050
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 50 50 50 50 50 50
## ..$ size_MB : int [1:6] 348 314 338 421 337 390
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971443" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971445" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971453" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/007784/SRR7971463" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:6] "SRP163900" "SRP163900" "SRP163900" "SRP163900" ...
## ..$ BioProject : chr [1:6] "PRJNA494882" "PRJNA494882" "PRJNA494882" "PRJNA494882" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 494882 494882 494882 494882 494882 494882
## ..$ Sample : chr [1:6] "SRS3883169" "SRS3883171" "SRS3883179" "SRS3883189" ...
## ..$ BioSample : chr [1:6] "SAMN10182762" "SAMN10182760" "SAMN10182752" "SAMN10182802" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA790151" "SRA790151" "SRA790151" "SRA790151" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "B443F450A468DF67817D89F122122F67" "080E96661C0B970A3CF57E5854E5E35F" "DFBC0434234BB46E6056B441FBAC7042" "16363EB5A844F8EA1CF38EEE02CC6523" ...
## ..$ ReadHash : chr [1:6] "22EF3357B85FD0ACA1DD2E4EDEB9FD88" "111F833FB9CBFB28F8C971DC68DAF955" "C1D98422A997EB2AFB6F0511E63019BB" "D076FFCE966B0856013EEDE2EF64BFAB" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP029281:alpha versus beta cells:alpha;SRX340815,SRX340817,SRX340819:beta;SRX340816,SRX340818,SRX340820;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR958701: int [1:58302] 26 11 5 3 0 0 10 23 10 29 ...
## ..$ SRR958702: int [1:58302] 19 1 2 0 0 0 0 10 2 17 ...
## ..$ SRR958703: int [1:58302] 8 23 6 0 0 0 0 16 0 2 ...
## ..$ SRR958704: int [1:58302] 6 62 9 0 0 0 0 7 0 4 ...
## ..$ SRR958705: int [1:58302] 2 27 9 4 0 0 0 2 0 0 ...
## ..$ SRR958706: int [1:58302] 2 10 9 2 0 0 0 2 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR958701: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958702: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958703: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958704: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958705: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958706: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR958701: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958702: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958703: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958704: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958705: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958706: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession: chr [1:6] "SRX340815" "SRX340816" "SRX340817" "SRX340818" ...
## ..$ SRS_accession: chr [1:6] "SRS474148" "SRS474150" "SRS474149" "SRS474151" ...
## ..$ SRP_accession: chr [1:6] "SRP029281" "SRP029281" "SRP029281" "SRP029281" ...
## ..$ Sample_name : chr [1:6] "GSM1217954" "GSM1217955" "GSM1217956" "GSM1217957" ...
## ..$ GEO_series : chr [1:6] "GSE50386" "GSE50386" "GSE50386" "GSE50386" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession : chr [1:6] "SRX340815" "SRX340816" "SRX340817" "SRX340818" ...
## ..$ SRS_accession : chr [1:6] "SRS474148" "SRS474150" "SRS474149" "SRS474151" ...
## ..$ SRP_accession : chr [1:6] "SRP029281" "SRP029281" "SRP029281" "SRP029281" ...
## ..$ Sample_name : chr [1:6] "GSM1217954" "GSM1217955" "GSM1217956" "GSM1217957" ...
## ..$ GEO_series : chr [1:6] "GSE50386" "GSE50386" "GSE50386" "GSE50386" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1217954" "GSM1217955" "GSM1217956" "GSM1217957" ...
## ..$ ReleaseDate : chr [1:6] "2015-07-22 17:04:08" "2015-07-22 17:04:08" "2015-07-22 17:04:05" "2015-07-22 17:04:05" ...
## ..$ LoadDate : chr [1:6] "2015-08-06 03:06:15" "2015-08-06 03:11:48" "2015-08-06 02:53:03" "2015-08-06 02:38:28" ...
## ..$ spots : int [1:6] 81365373 74954527 97704374 78508860 72405803 73291067
## ..$ bases : num [1:6] 8.14e+09 7.50e+09 9.77e+09 7.85e+09 7.24e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 100 100 100 100 100 100
## ..$ size_MB : int [1:6] 4823 4410 5706 4477 4102 4152
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958701/SRR958701.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958702/SRR958702.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958703/SRR958703.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958704/SRR958704.2" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP029281" "SRP029281" "SRP029281" "SRP029281" ...
## ..$ BioProject : chr [1:6] "PRJNA217397" "PRJNA217397" "PRJNA217397" "PRJNA217397" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 217397 217397 217397 217397 217397 217397
## ..$ Sample : chr [1:6] "SRS474148" "SRS474150" "SRS474149" "SRS474151" ...
## ..$ BioSample : chr [1:6] "SAMN02338337" "SAMN02338341" "SAMN02338340" "SAMN02338339" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA099314" "SRA099314" "SRA099314" "SRA099314" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "6A3312F270DCF0B9AA29C18363B7DAF4" "33B1725035B2A8FD8635336DDEA0550C" "20C6797AF4044DB0DFCD84A3FFE00EFF" "E2D24013CFA0B4A6EEC8626E02BCD0D4" ...
## ..$ ReadHash : chr [1:6] "6DC1D72C4761D960CB015076948E9147" "C0EA99847BA892272957B68C0190899E" "ECAEFFE962FD1544DBC5867F185CA5D4" "424328E1F7009940599AEC06A27A0CC4" ...
## $ absent : chr(0)## SRP029281:alpha versus exocrine cells:alpha;SRX340815,SRX340817,SRX340819:exocrine;SRX340821,SRX340822;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR958701: int [1:58302] 26 11 5 3 0 0 10 23 10 29 ...
## ..$ SRR958703: int [1:58302] 8 23 6 0 0 0 0 16 0 2 ...
## ..$ SRR958705: int [1:58302] 2 27 9 4 0 0 0 2 0 0 ...
## ..$ SRR958707: int [1:58302] 0 64 2 0 0 0 1 1 0 2 ...
## ..$ SRR958708: int [1:58302] 11 30 4 2 0 0 0 2 0 14 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR958701: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958703: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958705: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958707: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958708: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR958701: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958703: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958705: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958707: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958708: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession: chr [1:5] "SRX340815" "SRX340817" "SRX340819" "SRX340821" ...
## ..$ SRS_accession: chr [1:5] "SRS474148" "SRS474149" "SRS474152" "SRS474154" ...
## ..$ SRP_accession: chr [1:5] "SRP029281" "SRP029281" "SRP029281" "SRP029281" ...
## ..$ Sample_name : chr [1:5] "GSM1217954" "GSM1217956" "GSM1217958" "GSM1217960" ...
## ..$ GEO_series : chr [1:5] "GSE50386" "GSE50386" "GSE50386" "GSE50386" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession : chr [1:5] "SRX340815" "SRX340817" "SRX340819" "SRX340821" ...
## ..$ SRS_accession : chr [1:5] "SRS474148" "SRS474149" "SRS474152" "SRS474154" ...
## ..$ SRP_accession : chr [1:5] "SRP029281" "SRP029281" "SRP029281" "SRP029281" ...
## ..$ Sample_name : chr [1:5] "GSM1217954" "GSM1217956" "GSM1217958" "GSM1217960" ...
## ..$ GEO_series : chr [1:5] "GSE50386" "GSE50386" "GSE50386" "GSE50386" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM1217954" "GSM1217956" "GSM1217958" "GSM1217960" ...
## ..$ ReleaseDate : chr [1:5] "2015-07-22 17:04:08" "2015-07-22 17:04:05" "2015-07-22 17:04:05" "2015-07-22 17:04:05" ...
## ..$ LoadDate : chr [1:5] "2015-08-06 03:06:15" "2015-08-06 02:53:03" "2015-08-06 02:28:37" "2015-08-06 02:20:30" ...
## ..$ spots : int [1:5] 81365373 97704374 72405803 104980114 93127462
## ..$ bases : num [1:5] 8.14e+09 9.77e+09 7.24e+09 1.05e+10 9.31e+09
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 100 100 100 100 100
## ..$ size_MB : int [1:5] 4823 5706 4102 6529 5659
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958701/SRR958701.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958703/SRR958703.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958705/SRR958705.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958707/SRR958707.2" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:5] "SRP029281" "SRP029281" "SRP029281" "SRP029281" ...
## ..$ BioProject : chr [1:5] "PRJNA217397" "PRJNA217397" "PRJNA217397" "PRJNA217397" ...
## ..$ Study_Pubmed_id : int [1:5] 2 2 2 2 2
## ..$ ProjectID : int [1:5] 217397 217397 217397 217397 217397
## ..$ Sample : chr [1:5] "SRS474148" "SRS474149" "SRS474152" "SRS474154" ...
## ..$ BioSample : chr [1:5] "SAMN02338337" "SAMN02338340" "SAMN02338344" "SAMN02338342" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA099314" "SRA099314" "SRA099314" "SRA099314" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "6A3312F270DCF0B9AA29C18363B7DAF4" "20C6797AF4044DB0DFCD84A3FFE00EFF" "8A57C3DFF786D24D8518CD3542DD304E" "740312DB7BBEC35D21AC1864C8575F53" ...
## ..$ ReadHash : chr [1:5] "6DC1D72C4761D960CB015076948E9147" "ECAEFFE962FD1544DBC5867F185CA5D4" "8AFD77CE4F87CB797F519FCC2703C11D" "53542695A4910AD731AAD2153A85325B" ...
## $ absent : chr(0)## SRP029281:beta versus exocrine cells:beta;SRX340816,SRX340818,SRX340820:exocrine;SRX340821,SRX340822;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 5 variables:
## ..$ SRR958702: int [1:58302] 19 1 2 0 0 0 0 10 2 17 ...
## ..$ SRR958704: int [1:58302] 6 62 9 0 0 0 0 7 0 4 ...
## ..$ SRR958706: int [1:58302] 2 10 9 2 0 0 0 2 0 0 ...
## ..$ SRR958707: int [1:58302] 0 64 2 0 0 0 1 1 0 2 ...
## ..$ SRR958708: int [1:58302] 11 30 4 2 0 0 0 2 0 14 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR958702: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958704: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958706: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958707: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR958708: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 5 variables:
## ..$ SRR958702: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958704: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958706: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958707: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR958708: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession: chr [1:5] "SRX340816" "SRX340818" "SRX340820" "SRX340821" ...
## ..$ SRS_accession: chr [1:5] "SRS474150" "SRS474151" "SRS474153" "SRS474154" ...
## ..$ SRP_accession: chr [1:5] "SRP029281" "SRP029281" "SRP029281" "SRP029281" ...
## ..$ Sample_name : chr [1:5] "GSM1217955" "GSM1217957" "GSM1217959" "GSM1217960" ...
## ..$ GEO_series : chr [1:5] "GSE50386" "GSE50386" "GSE50386" "GSE50386" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession : chr [1:5] "SRX340816" "SRX340818" "SRX340820" "SRX340821" ...
## ..$ SRS_accession : chr [1:5] "SRS474150" "SRS474151" "SRS474153" "SRS474154" ...
## ..$ SRP_accession : chr [1:5] "SRP029281" "SRP029281" "SRP029281" "SRP029281" ...
## ..$ Sample_name : chr [1:5] "GSM1217955" "GSM1217957" "GSM1217959" "GSM1217960" ...
## ..$ GEO_series : chr [1:5] "GSE50386" "GSE50386" "GSE50386" "GSE50386" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM1217955" "GSM1217957" "GSM1217959" "GSM1217960" ...
## ..$ ReleaseDate : chr [1:5] "2015-07-22 17:04:08" "2015-07-22 17:04:05" "2015-07-22 17:04:05" "2015-07-22 17:04:05" ...
## ..$ LoadDate : chr [1:5] "2015-08-06 03:11:48" "2015-08-06 02:38:28" "2015-08-06 02:21:32" "2015-08-06 02:20:30" ...
## ..$ spots : int [1:5] 74954527 78508860 73291067 104980114 93127462
## ..$ bases : num [1:5] 7.50e+09 7.85e+09 7.33e+09 1.05e+10 9.31e+09
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 100 100 100 100 100
## ..$ size_MB : int [1:5] 4410 4477 4152 6529 5659
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958702/SRR958702.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958704/SRR958704.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958706/SRR958706.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR958707/SRR958707.2" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:5] "SRP029281" "SRP029281" "SRP029281" "SRP029281" ...
## ..$ BioProject : chr [1:5] "PRJNA217397" "PRJNA217397" "PRJNA217397" "PRJNA217397" ...
## ..$ Study_Pubmed_id : int [1:5] 2 2 2 2 2
## ..$ ProjectID : int [1:5] 217397 217397 217397 217397 217397
## ..$ Sample : chr [1:5] "SRS474150" "SRS474151" "SRS474153" "SRS474154" ...
## ..$ BioSample : chr [1:5] "SAMN02338341" "SAMN02338339" "SAMN02338338" "SAMN02338342" ...
## ..$ SampleType : chr [1:5] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:5] 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:5] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:5] NA NA NA NA NA
## ..$ source : logi [1:5] NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:5] NA NA NA NA NA
## ..$ Subject_ID : logi [1:5] NA NA NA NA NA
## ..$ Sex : logi [1:5] NA NA NA NA NA
## ..$ Disease : logi [1:5] NA NA NA NA NA
## ..$ Tumor : chr [1:5] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:5] NA NA NA NA NA
## ..$ Analyte_Type : logi [1:5] NA NA NA NA NA
## ..$ Histological_Type : logi [1:5] NA NA NA NA NA
## ..$ Body_Site : logi [1:5] NA NA NA NA NA
## ..$ CenterName : chr [1:5] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:5] "SRA099314" "SRA099314" "SRA099314" "SRA099314" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "33B1725035B2A8FD8635336DDEA0550C" "E2D24013CFA0B4A6EEC8626E02BCD0D4" "8F972DC4CBEBDFF3CB8620D126895649" "740312DB7BBEC35D21AC1864C8575F53" ...
## ..$ ReadHash : chr [1:5] "C0EA99847BA892272957B68C0190899E" "424328E1F7009940599AEC06A27A0CC4" "7BD78FB48C172A9FFFBB47A1667E65A3" "53542695A4910AD731AAD2153A85325B" ...
## $ absent : chr(0)## SRP121799:diabetic versus non-diabetic CMSC:diabetic;SRX3327085,SRX3327086, SRX3327087,SRX3327088,SRX3327089,SRX3327090,SRX3327091:non-diabetic;SRX3327092,SRX3327093,SRX3327094,SRX3327095,SRX3327096,SRX3327097,SRX3327098;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 14 variables:
## ..$ SRR6218466: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218467: int [1:58302] 0 12 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218468: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218469: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR6218470: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218471: int [1:58302] 0 18 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218472: int [1:58302] 0 9 1 0 0 0 0 0 0 0 ...
## ..$ SRR6218473: int [1:58302] 0 10 2 0 0 0 0 0 0 1 ...
## ..$ SRR6218474: int [1:58302] 0 7 3 0 0 0 0 0 0 1 ...
## ..$ SRR6218475: int [1:58302] 0 17 2 0 0 0 0 0 0 0 ...
## ..$ SRR6218476: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218477: int [1:58302] 0 24 2 1 0 0 0 0 0 1 ...
## ..$ SRR6218478: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218479: int [1:58302] 0 9 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 14 variables:
## ..$ SRR6218466: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218467: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218468: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218469: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218470: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218471: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218472: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218473: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218474: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218475: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218476: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218477: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218478: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6218479: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 14 variables:
## ..$ SRR6218466: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "75" ...
## ..$ SRR6218467: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "76" ...
## ..$ SRR6218468: chr [1:30] "PE" "Sanger/Illumina1.9" "71" "76" ...
## ..$ SRR6218469: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "75" ...
## ..$ SRR6218470: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "75" ...
## ..$ SRR6218471: chr [1:30] "PE" "Sanger/Illumina1.9" "66" "76" ...
## ..$ SRR6218472: chr [1:30] "PE" "Sanger/Illumina1.9" "68" "76" ...
## ..$ SRR6218473: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "76" ...
## ..$ SRR6218474: chr [1:30] "PE" "Sanger/Illumina1.9" "68" "76" ...
## ..$ SRR6218475: chr [1:30] "PE" "Sanger/Illumina1.9" "68" "76" ...
## ..$ SRR6218476: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "75" ...
## ..$ SRR6218477: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "76" ...
## ..$ SRR6218478: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "75" ...
## ..$ SRR6218479: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "75" ...
## $ MetadataSummary:'data.frame': 14 obs. of 7 variables:
## ..$ QC_summary : chr [1:14] "WARN(5,7)" "WARN(4,6)" "WARN(6)" "PASS" ...
## ..$ SRX_accession: chr [1:14] "SRX3327085" "SRX3327086" "SRX3327087" "SRX3327088" ...
## ..$ SRS_accession: chr [1:14] "SRS2630688" "SRS2630689" "SRS2630690" "SRS2630691" ...
## ..$ SRP_accession: chr [1:14] "SRP121799" "SRP121799" "SRP121799" "SRP121799" ...
## ..$ Sample_name : chr [1:14] "GSM2831016" "GSM2831017" "GSM2831018" "GSM2831019" ...
## ..$ GEO_series : chr [1:14] "GSE106177" "GSE106177" "GSE106177" "GSE106177" ...
## ..$ Library_name : logi [1:14] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 14 obs. of 52 variables:
## ..$ QC_summary : chr [1:14] "WARN(5,7)" "WARN(4,6)" "WARN(6)" "PASS" ...
## ..$ SRX_accession : chr [1:14] "SRX3327085" "SRX3327086" "SRX3327087" "SRX3327088" ...
## ..$ SRS_accession : chr [1:14] "SRS2630688" "SRS2630689" "SRS2630690" "SRS2630691" ...
## ..$ SRP_accession : chr [1:14] "SRP121799" "SRP121799" "SRP121799" "SRP121799" ...
## ..$ Sample_name : chr [1:14] "GSM2831016" "GSM2831017" "GSM2831018" "GSM2831019" ...
## ..$ GEO_series : chr [1:14] "GSE106177" "GSE106177" "GSE106177" "GSE106177" ...
## ..$ Library_name : logi [1:14] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:14] "GSM2831016" "GSM2831017" "GSM2831018" "GSM2831019" ...
## ..$ ReleaseDate : chr [1:14] "2018-10-31 16:42:16" "2018-10-31 16:42:16" "2018-10-31 16:42:16" "2018-10-31 16:42:16" ...
## ..$ LoadDate : chr [1:14] "2017-10-25 21:26:46" "2017-10-25 21:41:02" "2017-10-25 21:43:53" "2017-10-25 21:26:25" ...
## ..$ spots : int [1:14] 14921850 31875594 33713689 17924797 18012488 32861648 33826908 31991769 26288870 31483295 ...
## ..$ bases : num [1:14] 2.21e+09 4.74e+09 5.00e+09 2.66e+09 2.67e+09 ...
## ..$ spots_with_mates : int [1:14] 14921850 31875594 33713689 17924797 18012488 32861648 33826908 31991769 26288870 31483295 ...
## ..$ avgLength : int [1:14] 148 148 148 148 148 147 148 147 148 147 ...
## ..$ size_MB : int [1:14] 909 1790 1889 1086 1083 1838 1896 1782 1473 1766 ...
## ..$ AssemblyName : logi [1:14] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:14] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6218466/SRR6218466.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6218467/SRR6218467.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6218468/SRR6218468.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6218469/SRR6218469.1" ...
## ..$ LibraryName : logi [1:14] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:14] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:14] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:14] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:14] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:14] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:14] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:14] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:14] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:14] "SRP121799" "SRP121799" "SRP121799" "SRP121799" ...
## ..$ BioProject : chr [1:14] "PRJNA415889" "PRJNA415889" "PRJNA415889" "PRJNA415889" ...
## ..$ Study_Pubmed_id : int [1:14] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:14] 415889 415889 415889 415889 415889 415889 415889 415889 415889 415889 ...
## ..$ Sample : chr [1:14] "SRS2630688" "SRS2630689" "SRS2630690" "SRS2630691" ...
## ..$ BioSample : chr [1:14] "SAMN07835726" "SAMN07835718" "SAMN07835716" "SAMN07835713" ...
## ..$ SampleType : chr [1:14] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:14] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:14] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:14] NA NA NA NA NA NA ...
## ..$ source : logi [1:14] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:14] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:14] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:14] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:14] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:14] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:14] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:14] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:14] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:14] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:14] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:14] "SRA624879" "SRA624879" "SRA624879" "SRA624879" ...
## ..$ dbgap_study_accession: logi [1:14] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:14] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:14] "129AAC19E400641C832CB5A61A06C177" "7436228118E9C944AE4BC464F9DF933C" "684F398A75AEA488135DA6653623942D" "0475410B82D0F89C5EFAD288A2DF52AA" ...
## ..$ ReadHash : chr [1:14] "FEE3D0808D1A6E17C2ACD115C787079B" "95D7176D71F10C05EFB320590DEC480B" "53DFA21CAF89AF6D751F7FD1DE82BDF8" "B6B7EE6F4E43D863CD258015FCED0181" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 31 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP081605: Genes expressed differentially in whole blood samples in responders vs control in teplizumab treatment after 6 months:Ctrl; SRX2018880,SRX2018882,SRX2018885,SRX2018887,SRX2018889,SRX2018892,SRX2018895,SRX2018896,SRX2018897,SRX2018905, SRX2018908,SRX2018909,SRX2018911,SRX2018913,SRX2018914:Responders; SRX2018890,SRX2018891,SRX2018893,SRX2018900, SRX2018901,SRX2018902,SRX2018906,SRX2018910,SRX2018915,SRX2018916,SRX2018919,SRX2018920,SRX2018875,SRX2018876, SRX2018884,SRX2018888## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 30 variables:
## ..$ SRR4026918: int [1:58302] 2 2 0 0 0 0 0 0 0 2 ...
## ..$ SRR4026919: int [1:58302] 1 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR4026925: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026927: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026928: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026930: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026931: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026932: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026933: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026934: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026935: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026936: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026938: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026939: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026940: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026943: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026944: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026945: int [1:58302] 1 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026948: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026949: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026951: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026952: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026953: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026954: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026956: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026957: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026958: int [1:58302] 1 11 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026959: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026962: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026963: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 30 variables:
## ..$ SRR4026918: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026919: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026925: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026927: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026928: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026930: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026931: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026932: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026933: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026934: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026935: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026936: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026938: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026939: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026940: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026943: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026944: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026945: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026948: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026949: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026951: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026952: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026953: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026954: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026956: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026957: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026958: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026959: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026962: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026963: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 30 variables:
## ..$ SRR4026918: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026919: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026925: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026927: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026928: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026930: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026931: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026932: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026933: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026934: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026935: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026936: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026938: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026939: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026940: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026943: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026944: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026945: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026948: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026949: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026951: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026952: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026953: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026954: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026956: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026957: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026958: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026959: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026962: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026963: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 30 obs. of 7 variables:
## ..$ QC_summary : chr [1:30] "WARN(5)" "WARN(5,7)" "PASS" "WARN(5)" ...
## ..$ SRX_accession: chr [1:30] "SRX2018875" "SRX2018876" "SRX2018882" "SRX2018884" ...
## ..$ SRS_accession: chr [1:30] "SRS1614728" "SRS1614729" "SRS1614735" "SRS1614737" ...
## ..$ SRP_accession: chr [1:30] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:30] "GSM2275066" "GSM2275067" "GSM2275073" "GSM2275075" ...
## ..$ GEO_series : chr [1:30] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:30] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 30 obs. of 52 variables:
## ..$ QC_summary : chr [1:30] "WARN(5)" "WARN(5,7)" "PASS" "WARN(5)" ...
## ..$ SRX_accession : chr [1:30] "SRX2018875" "SRX2018876" "SRX2018882" "SRX2018884" ...
## ..$ SRS_accession : chr [1:30] "SRS1614728" "SRS1614729" "SRS1614735" "SRS1614737" ...
## ..$ SRP_accession : chr [1:30] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:30] "GSM2275066" "GSM2275067" "GSM2275073" "GSM2275075" ...
## ..$ GEO_series : chr [1:30] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:30] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:30] "GSM2275066" "GSM2275067" "GSM2275073" "GSM2275075" ...
## ..$ ReleaseDate : chr [1:30] "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" ...
## ..$ LoadDate : chr [1:30] "2016-08-12 18:08:58" "2016-08-12 18:06:16" "2016-08-12 18:06:43" "2016-08-12 18:06:44" ...
## ..$ spots : int [1:30] 12785215 11633165 14807391 14601701 11911388 11038105 12712228 14403915 12651666 14344202 ...
## ..$ bases : int [1:30] 652045965 593291415 755176941 744686751 607480788 562943355 648323628 734599665 645234966 731554302 ...
## ..$ spots_with_mates : int [1:30] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:30] 51 51 51 51 51 51 51 51 51 51 ...
## ..$ size_MB : int [1:30] 414 377 479 474 387 362 421 475 419 471 ...
## ..$ AssemblyName : logi [1:30] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:30] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026918/SRR4026918.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026919/SRR4026919.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026925/SRR4026925.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026927/SRR4026927.1" ...
## ..$ LibraryName : logi [1:30] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:30] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:30] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:30] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:30] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:30] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:30] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:30] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:30] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:30] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ BioProject : chr [1:30] "PRJNA338797" "PRJNA338797" "PRJNA338797" "PRJNA338797" ...
## ..$ Study_Pubmed_id : logi [1:30] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:30] 338797 338797 338797 338797 338797 338797 338797 338797 338797 338797 ...
## ..$ Sample : chr [1:30] "SRS1614728" "SRS1614729" "SRS1614735" "SRS1614737" ...
## ..$ BioSample : chr [1:30] "SAMN05571045" "SAMN05571044" "SAMN05571038" "SAMN05570716" ...
## ..$ SampleType : chr [1:30] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:30] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:30] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:30] NA NA NA NA NA NA ...
## ..$ source : logi [1:30] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:30] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:30] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:30] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:30] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:30] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:30] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:30] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:30] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:30] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:30] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:30] "SRA452046" "SRA452046" "SRA452046" "SRA452046" ...
## ..$ dbgap_study_accession: logi [1:30] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:30] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:30] "258127E853E4BB4DE925B6213D1F1302" "4FB9008B3AAA10FC699E24F64BB33D91" "EA4E070996AAD0811800B75D1C9ACC30" "8BCFEF91EF9711DFDB20CF6791D703A8" ...
## ..$ ReadHash : chr [1:30] "85AADE67865718FFC4FD55F91884CBE2" "615E0FC7D021505EB8811C82378248F9" "46EC1B67BB9EA868178E6EA71746F2A7" "51FAC4C23A16DB65346D28C393F621B2" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 170 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP081605: Genes expressed differentially in whole blood samples in responders vs non-responders in teplizumab treatment after 6 months:Non-responders; SRX2018922,SRX2018877,SRX2018878,SRX2018879,SRX2018881,SRX2018883,SRX2018886,SRX2018894, SRX2018898, SRX2018899,SRX2018903,SRX2018904,SRX2018907,SRX2018912, SRX2018917,SRX2018921,SRX2018918:Responders; SRX2018890,SRX2018891,SRX2018893,SRX2018900,SRX2018901,SRX2018902,SRX2018906,SRX2018910,SRX2018915,SRX2018916,SRX2018919,SRX2018920,SRX2018875,SRX2018876,SRX2018884,SRX2018888## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 33 variables:
## ..$ SRR4026918: int [1:58302] 2 2 0 0 0 0 0 0 0 2 ...
## ..$ SRR4026919: int [1:58302] 1 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR4026920: int [1:58302] 0 0 0 0 0 0 0 0 0 2 ...
## ..$ SRR4026921: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026922: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026924: int [1:58302] 0 0 0 0 0 0 0 0 0 4 ...
## ..$ SRR4026926: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026927: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026929: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026931: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026933: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026934: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026936: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026937: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026941: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026942: int [1:58302] 0 2 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026943: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026944: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026945: int [1:58302] 1 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026946: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026947: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026949: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026950: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026953: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026955: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026958: int [1:58302] 1 11 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026959: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026960: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026961: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026962: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026963: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026964: int [1:58302] 0 0 0 0 0 0 0 0 0 2 ...
## ..$ SRR4026965: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 33 variables:
## ..$ SRR4026918: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026919: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026920: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026921: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026922: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026924: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026926: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026927: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026929: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026931: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026933: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026934: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026936: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026937: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026941: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026942: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026943: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026944: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026945: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026946: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026947: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026949: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026950: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026953: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026955: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026958: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026959: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026960: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026961: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026962: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026963: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026964: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026965: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 33 variables:
## ..$ SRR4026918: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026919: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026920: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026921: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026922: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026924: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026926: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026927: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026929: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026931: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026933: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026934: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026936: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026937: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026941: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026942: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026943: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026944: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026945: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026946: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026947: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026949: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026950: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026953: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026955: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026958: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026959: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026960: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026961: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026962: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026963: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026964: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR4026965: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 33 obs. of 7 variables:
## ..$ QC_summary : chr [1:33] "WARN(5)" "WARN(5,7)" "WARN(5,7)" "WARN(3,4,5,6,7)" ...
## ..$ SRX_accession: chr [1:33] "SRX2018875" "SRX2018876" "SRX2018877" "SRX2018878" ...
## ..$ SRS_accession: chr [1:33] "SRS1614728" "SRS1614729" "SRS1614730" "SRS1614731" ...
## ..$ SRP_accession: chr [1:33] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:33] "GSM2275066" "GSM2275067" "GSM2275068" "GSM2275069" ...
## ..$ GEO_series : chr [1:33] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:33] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 33 obs. of 52 variables:
## ..$ QC_summary : chr [1:33] "WARN(5)" "WARN(5,7)" "WARN(5,7)" "WARN(3,4,5,6,7)" ...
## ..$ SRX_accession : chr [1:33] "SRX2018875" "SRX2018876" "SRX2018877" "SRX2018878" ...
## ..$ SRS_accession : chr [1:33] "SRS1614728" "SRS1614729" "SRS1614730" "SRS1614731" ...
## ..$ SRP_accession : chr [1:33] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:33] "GSM2275066" "GSM2275067" "GSM2275068" "GSM2275069" ...
## ..$ GEO_series : chr [1:33] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:33] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:33] "GSM2275066" "GSM2275067" "GSM2275068" "GSM2275069" ...
## ..$ ReleaseDate : chr [1:33] "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" ...
## ..$ LoadDate : chr [1:33] "2016-08-12 18:08:58" "2016-08-12 18:06:16" "2016-08-12 18:05:54" "2016-08-12 18:06:19" ...
## ..$ spots : int [1:33] 12785215 11633165 10729270 11812171 10851082 9997372 18320321 14601701 11904201 12712228 ...
## ..$ bases : int [1:33] 652045965 593291415 547192770 602420721 553405182 509865972 934336371 744686751 607114251 648323628 ...
## ..$ spots_with_mates : int [1:33] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:33] 51 51 51 51 51 51 51 51 51 51 ...
## ..$ size_MB : int [1:33] 414 377 349 390 352 324 595 474 385 421 ...
## ..$ AssemblyName : logi [1:33] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:33] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026918/SRR4026918.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026919/SRR4026919.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026920/SRR4026920.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026921/SRR4026921.1" ...
## ..$ LibraryName : logi [1:33] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:33] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:33] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:33] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:33] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:33] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:33] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:33] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:33] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:33] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ BioProject : chr [1:33] "PRJNA338797" "PRJNA338797" "PRJNA338797" "PRJNA338797" ...
## ..$ Study_Pubmed_id : logi [1:33] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:33] 338797 338797 338797 338797 338797 338797 338797 338797 338797 338797 ...
## ..$ Sample : chr [1:33] "SRS1614728" "SRS1614729" "SRS1614730" "SRS1614731" ...
## ..$ BioSample : chr [1:33] "SAMN05571045" "SAMN05571044" "SAMN05571043" "SAMN05571042" ...
## ..$ SampleType : chr [1:33] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:33] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:33] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:33] NA NA NA NA NA NA ...
## ..$ source : logi [1:33] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:33] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:33] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:33] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:33] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:33] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:33] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:33] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:33] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:33] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:33] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:33] "SRA452046" "SRA452046" "SRA452046" "SRA452046" ...
## ..$ dbgap_study_accession: logi [1:33] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:33] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:33] "258127E853E4BB4DE925B6213D1F1302" "4FB9008B3AAA10FC699E24F64BB33D91" "0C9E507EF5C8D39E06E37FFF70ED50A0" "1F3BDC75C8CD02E2EE376E49DB927BC5" ...
## ..$ ReadHash : chr [1:33] "85AADE67865718FFC4FD55F91884CBE2" "615E0FC7D021505EB8811C82378248F9" "FF8F3A71BD821495EA2CD6A2C4D3A4B8" "554620FB2B94408C68746B5E1ADCB145" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 170 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP081605: Genes expressed differentially in whole blood samples in responders vs control in teplizumab treatment after 12 months:Ctrl; SRX2018789,SRX2018791,SRX2018793,SRX2018795,SRX2018797,SRX2018798,SRX2018801,SRX2018802,SRX2018805,SRX2018806, SRX2018807,SRX2018810,SRX2018817,SRX2018818,SRX2018823,SRX2018826:Responders; SRX2018814,SRX2018816,SRX2018819,SRX2018820, SRX2018824,SRX2018825,SRX2018827,SRX2018813,SRX2018787,SRX2018799,SRX2018803,SRX2018808,SRX2018809## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 28 variables:
## ..$ SRR4026830: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026834: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026836: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026838: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026840: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026841: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026842: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026844: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026845: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026846: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026848: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026849: int [1:58302] 0 0 0 1 0 0 0 0 0 0 ...
## ..$ SRR4026850: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026851: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026852: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026853: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026856: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026857: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026859: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026860: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026861: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026862: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026863: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026866: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026867: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026868: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026869: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026870: int [1:58302] 1 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 28 variables:
## ..$ SRR4026830: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026834: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026836: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026838: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026840: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026841: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026842: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026844: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026845: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026846: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026848: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026849: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026850: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026851: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026852: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026853: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026856: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026857: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026859: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026860: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026861: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026862: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026863: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026866: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026867: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026868: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026869: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026870: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 28 variables:
## ..$ SRR4026830: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026834: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026836: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026838: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026840: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026841: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026842: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026844: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026845: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026846: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026848: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026849: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026850: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026851: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026852: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026853: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026856: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026857: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026859: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026860: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026861: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026862: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026863: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026866: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026867: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026868: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026869: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026870: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 28 obs. of 7 variables:
## ..$ QC_summary : chr [1:28] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:28] "SRX2018787" "SRX2018791" "SRX2018793" "SRX2018795" ...
## ..$ SRS_accession: chr [1:28] "SRS1614640" "SRS1614644" "SRS1614646" "SRS1614648" ...
## ..$ SRP_accession: chr [1:28] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:28] "GSM2274978" "GSM2274982" "GSM2274984" "GSM2274986" ...
## ..$ GEO_series : chr [1:28] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:28] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 28 obs. of 52 variables:
## ..$ QC_summary : chr [1:28] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:28] "SRX2018787" "SRX2018791" "SRX2018793" "SRX2018795" ...
## ..$ SRS_accession : chr [1:28] "SRS1614640" "SRS1614644" "SRS1614646" "SRS1614648" ...
## ..$ SRP_accession : chr [1:28] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:28] "GSM2274978" "GSM2274982" "GSM2274984" "GSM2274986" ...
## ..$ GEO_series : chr [1:28] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:28] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:28] "GSM2274978" "GSM2274982" "GSM2274984" "GSM2274986" ...
## ..$ ReleaseDate : chr [1:28] "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" ...
## ..$ LoadDate : chr [1:28] "2016-08-12 18:03:09" "2016-08-12 18:03:12" "2016-08-12 18:03:12" "2016-08-12 18:03:07" ...
## ..$ spots : int [1:28] 5191621 4800542 4693109 5302271 4810394 5550529 4876331 6895654 5896729 6747354 ...
## ..$ bases : int [1:28] 259581050 240027100 234655450 265113550 240519700 277526450 243816550 344782700 294836450 337367700 ...
## ..$ spots_with_mates : int [1:28] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:28] 50 50 50 50 50 50 50 50 50 50 ...
## ..$ size_MB : int [1:28] 152 141 138 156 141 162 143 204 174 198 ...
## ..$ AssemblyName : logi [1:28] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:28] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026830/SRR4026830.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026834/SRR4026834.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026836/SRR4026836.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026838/SRR4026838.1" ...
## ..$ LibraryName : logi [1:28] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:28] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:28] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:28] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:28] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:28] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:28] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:28] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:28] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:28] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ BioProject : chr [1:28] "PRJNA338797" "PRJNA338797" "PRJNA338797" "PRJNA338797" ...
## ..$ Study_Pubmed_id : logi [1:28] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:28] 338797 338797 338797 338797 338797 338797 338797 338797 338797 338797 ...
## ..$ Sample : chr [1:28] "SRS1614640" "SRS1614644" "SRS1614646" "SRS1614648" ...
## ..$ BioSample : chr [1:28] "SAMN05570893" "SAMN05570889" "SAMN05571097" "SAMN05571095" ...
## ..$ SampleType : chr [1:28] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:28] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:28] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:28] NA NA NA NA NA NA ...
## ..$ source : logi [1:28] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:28] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:28] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:28] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:28] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:28] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:28] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:28] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:28] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:28] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:28] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:28] "SRA452046" "SRA452046" "SRA452046" "SRA452046" ...
## ..$ dbgap_study_accession: logi [1:28] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:28] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:28] "D4CC2DCBB7C4DE6D152CC045D5DC61D6" "5305080A896665C361BE73A60D6B1DA3" "9216F3050B0F07AC07A4E5D64FC0D3CC" "80A496FE871AAD8EDCE04E62237C8943" ...
## ..$ ReadHash : chr [1:28] "872E126C0DBCD51C79C50A2C9B273C2E" "B31A77DD665550A3832D8A780391FAC7" "29C6C8ACAA54CF4E400B0A242F8D004B" "D44C14F4ECCF24F1F11C5F8AB8A41162" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 40 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP081605: Genes expressed differentially in whole blood samples in responders vs non-responders in teplizumab treatment after 12 months:Non-responders; SRX2018788,SRX2018790,SRX2018792,SRX2018794,SRX2018796,SRX2018800,SRX2018804,SRX2018811,SRX2018812,SRX2018815,SRX2018821,SRX2018822,SRX2018828,SRX2018829:Responders;SRX2018814,SRX2018816,SRX2018819,SRX2018820, SRX2018824,SRX2018825,SRX2018827,SRX2018813,SRX2018787,SRX2018799,SRX2018803,SRX2018808,SRX2018809## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 27 variables:
## ..$ SRR4026830: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026831: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026833: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026835: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026837: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026839: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026842: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026843: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026846: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026847: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026851: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026852: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026854: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026855: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026856: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026857: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026858: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026859: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026862: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026863: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026864: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026865: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026867: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026868: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026870: int [1:58302] 1 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026871: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026872: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 27 variables:
## ..$ SRR4026830: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026831: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026833: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026835: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026837: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026839: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026842: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026843: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026846: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026847: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026851: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026852: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026854: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026855: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026856: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026857: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026858: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026859: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026862: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026863: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026864: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026865: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026867: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026868: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026870: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026871: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026872: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 27 variables:
## ..$ SRR4026830: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026831: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026833: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026835: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026837: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026839: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026842: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026843: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026846: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026847: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026851: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026852: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026854: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026855: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026856: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026857: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026858: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026859: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026862: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026863: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026864: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026865: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026867: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026868: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026870: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026871: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026872: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 27 obs. of 7 variables:
## ..$ QC_summary : chr [1:27] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:27] "SRX2018787" "SRX2018788" "SRX2018790" "SRX2018792" ...
## ..$ SRS_accession: chr [1:27] "SRS1614640" "SRS1614641" "SRS1614643" "SRS1614645" ...
## ..$ SRP_accession: chr [1:27] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:27] "GSM2274978" "GSM2274979" "GSM2274981" "GSM2274983" ...
## ..$ GEO_series : chr [1:27] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:27] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 27 obs. of 52 variables:
## ..$ QC_summary : chr [1:27] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:27] "SRX2018787" "SRX2018788" "SRX2018790" "SRX2018792" ...
## ..$ SRS_accession : chr [1:27] "SRS1614640" "SRS1614641" "SRS1614643" "SRS1614645" ...
## ..$ SRP_accession : chr [1:27] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:27] "GSM2274978" "GSM2274979" "GSM2274981" "GSM2274983" ...
## ..$ GEO_series : chr [1:27] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:27] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:27] "GSM2274978" "GSM2274979" "GSM2274981" "GSM2274983" ...
## ..$ ReleaseDate : chr [1:27] "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" ...
## ..$ LoadDate : chr [1:27] "2016-08-12 18:03:09" "2016-08-12 18:03:09" "2016-08-12 18:03:27" "2016-08-12 18:03:06" ...
## ..$ spots : int [1:27] 5191621 5341130 6146805 4468989 4552222 4278955 4876331 4608225 6747354 4977095 ...
## ..$ bases : int [1:27] 259581050 267056500 307340250 223449450 227611100 213947750 243816550 230411250 337367700 248854750 ...
## ..$ spots_with_mates : int [1:27] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:27] 50 50 50 50 50 50 50 50 50 50 ...
## ..$ size_MB : int [1:27] 152 158 180 131 133 126 143 140 198 149 ...
## ..$ AssemblyName : logi [1:27] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:27] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026830/SRR4026830.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026831/SRR4026831.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026833/SRR4026833.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026835/SRR4026835.1" ...
## ..$ LibraryName : logi [1:27] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:27] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:27] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:27] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:27] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:27] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:27] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:27] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:27] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:27] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ BioProject : chr [1:27] "PRJNA338797" "PRJNA338797" "PRJNA338797" "PRJNA338797" ...
## ..$ Study_Pubmed_id : logi [1:27] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:27] 338797 338797 338797 338797 338797 338797 338797 338797 338797 338797 ...
## ..$ Sample : chr [1:27] "SRS1614640" "SRS1614641" "SRS1614643" "SRS1614645" ...
## ..$ BioSample : chr [1:27] "SAMN05570893" "SAMN05570892" "SAMN05570890" "SAMN05570888" ...
## ..$ SampleType : chr [1:27] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:27] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:27] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:27] NA NA NA NA NA NA ...
## ..$ source : logi [1:27] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:27] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:27] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:27] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:27] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:27] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:27] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:27] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:27] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:27] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:27] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:27] "SRA452046" "SRA452046" "SRA452046" "SRA452046" ...
## ..$ dbgap_study_accession: logi [1:27] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:27] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:27] "D4CC2DCBB7C4DE6D152CC045D5DC61D6" "ED5888EBD5EE7A0F71267F95CE0070F9" "44BA301A487556F700B5992AE8DFBAEF" "220FE43F01B01206A83A186A5A7B7F43" ...
## ..$ ReadHash : chr [1:27] "872E126C0DBCD51C79C50A2C9B273C2E" "4FC0203B074EEE96E5A5F009C47862A7" "37CD4DD1D41693A48C2219DE70FE9943" "B50F076EDD78B884150E794FB306A2C3" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 20 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP081605: Genes expressed differentially in whole blood samples in responders vs control in teplizumab treatment after 24 months:Ctrl; SRX2018923,SRX2018929,SRX2018932,SRX2018935,SRX2018937,SRX2018941,SRX2018943,SRX2018945,SRX2018953, SRX2018956, SRX2018959,SRX2018960,SRX2018961,SRX2018964,SRX2018965,SRX2018968,SRX2018973:Responders; SRX2018924,SRX2018931,SRX2018936, SRX2018938,SRX2018939,SRX2018940,SRX2018942,SRX2018948,SRX2018949,SRX2018950,SRX2018954,SRX2018957, SRX2018966,SRX2018967,SRX2018970,SRX2018971,SRX2018972## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 33 variables:
## ..$ SRR4026967: int [1:58302] 0 1 0 2 0 0 0 0 0 0 ...
## ..$ SRR4026972: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026974: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026975: int [1:58302] 0 0 0 0 0 0 0 0 0 2 ...
## ..$ SRR4026978: int [1:58302] 0 0 0 1 0 0 0 0 0 0 ...
## ..$ SRR4026979: int [1:58302] 0 5 0 0 0 0 0 0 0 2 ...
## ..$ SRR4026980: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026981: int [1:58302] 0 4 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026982: int [1:58302] 1 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026983: int [1:58302] 0 4 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026984: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026985: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026986: int [1:58302] 2 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026988: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026991: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026992: int [1:58302] 1 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026993: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026996: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026997: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026999: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027000: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027002: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027003: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027004: int [1:58302] 1 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027007: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027008: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027009: int [1:58302] 1 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027010: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027011: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027013: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027014: int [1:58302] 1 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR4027015: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027016: int [1:58302] 1 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 33 variables:
## ..$ SRR4026967: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026972: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026974: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026975: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026978: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026982: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026983: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026984: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026985: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026986: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026988: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026991: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026992: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026993: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026996: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026997: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026999: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027000: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027002: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027003: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027004: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027007: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027008: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027009: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027010: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027011: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027013: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027014: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027015: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027016: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 33 variables:
## ..$ SRR4026967: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026972: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026974: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026975: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026978: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026979: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026980: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026981: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026982: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026983: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026984: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026985: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026986: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026988: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026991: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026992: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026993: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026996: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026997: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026999: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027000: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027002: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027003: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027004: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027007: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027008: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027009: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027010: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027011: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027013: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027014: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027015: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027016: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 33 obs. of 7 variables:
## ..$ QC_summary : chr [1:33] "WARN(5)" "WARN(5)" "WARN(5,7)" "WARN(5)" ...
## ..$ SRX_accession: chr [1:33] "SRX2018924" "SRX2018929" "SRX2018931" "SRX2018932" ...
## ..$ SRS_accession: chr [1:33] "SRS1614777" "SRS1614782" "SRS1614784" "SRS1614785" ...
## ..$ SRP_accession: chr [1:33] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:33] "GSM2275115" "GSM2275120" "GSM2275122" "GSM2275123" ...
## ..$ GEO_series : chr [1:33] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:33] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 33 obs. of 52 variables:
## ..$ QC_summary : chr [1:33] "WARN(5)" "WARN(5)" "WARN(5,7)" "WARN(5)" ...
## ..$ SRX_accession : chr [1:33] "SRX2018924" "SRX2018929" "SRX2018931" "SRX2018932" ...
## ..$ SRS_accession : chr [1:33] "SRS1614777" "SRS1614782" "SRS1614784" "SRS1614785" ...
## ..$ SRP_accession : chr [1:33] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:33] "GSM2275115" "GSM2275120" "GSM2275122" "GSM2275123" ...
## ..$ GEO_series : chr [1:33] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:33] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:33] "GSM2275115" "GSM2275120" "GSM2275122" "GSM2275123" ...
## ..$ ReleaseDate : chr [1:33] "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" ...
## ..$ LoadDate : chr [1:33] "2016-08-12 18:08:03" "2016-08-12 18:07:57" "2016-08-12 18:07:38" "2016-08-12 18:08:06" ...
## ..$ spots : int [1:33] 13229876 12291504 10942190 12210476 11499712 11505927 13473368 14339012 12557527 11604387 ...
## ..$ bases : int [1:33] 661493800 614575200 547109500 610523800 574985600 575296350 673668400 716950600 627876350 580219350 ...
## ..$ spots_with_mates : int [1:33] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:33] 50 50 50 50 50 50 50 50 50 50 ...
## ..$ size_MB : int [1:33] 417 387 343 384 364 364 426 452 399 365 ...
## ..$ AssemblyName : logi [1:33] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:33] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026967/SRR4026967.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026972/SRR4026972.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026974/SRR4026974.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026975/SRR4026975.1" ...
## ..$ LibraryName : logi [1:33] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:33] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:33] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:33] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:33] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:33] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:33] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:33] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:33] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:33] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ BioProject : chr [1:33] "PRJNA338797" "PRJNA338797" "PRJNA338797" "PRJNA338797" ...
## ..$ Study_Pubmed_id : logi [1:33] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:33] 338797 338797 338797 338797 338797 338797 338797 338797 338797 338797 ...
## ..$ Sample : chr [1:33] "SRS1614777" "SRS1614782" "SRS1614784" "SRS1614785" ...
## ..$ BioSample : chr [1:33] "SAMN05570761" "SAMN05570756" "SAMN05570754" "SAMN05570753" ...
## ..$ SampleType : chr [1:33] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:33] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:33] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:33] NA NA NA NA NA NA ...
## ..$ source : logi [1:33] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:33] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:33] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:33] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:33] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:33] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:33] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:33] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:33] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:33] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:33] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:33] "SRA452046" "SRA452046" "SRA452046" "SRA452046" ...
## ..$ dbgap_study_accession: logi [1:33] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:33] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:33] "0EC164F8786F8A81BA54A847C4482163" "DEC517276206890EF6B6F38A37D08BDB" "029A1D32A5F9D196B0EDEFA66B9F3229" "067CB0E0BD24919E2211097418E89FF8" ...
## ..$ ReadHash : chr [1:33] "665464FDC987222004CECFF6DE33564D" "3ADBEE3266BCDC3F16B494C3845E85DC" "06BE1BAD142936190EFA6D348A4B25AB" "88BD0EC6CAAADC80CC2C7BB1A84F65DD" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 26 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP081605: Genes expressed differentially in whole blood samples in responders vs non-responders in teplizumab treatment after 24 months:non-responders; SRX2018925,SRX2018926,SRX2018927,SRX2018928,SRX2018930,SRX2018933,SRX2018934,SRX2018944,SRX2018946,SRX2018947,SRX2018951,SRX2018952,SRX2018955,SRX2018958,SRX2018962,SRX2018963,SRX2018969,SRX2018974,SRX2018975,SRX2018976:Responders; SRX2018924,SRX2018931,SRX2018936,SRX2018938,SRX2018939,SRX2018940,SRX2018942,SRX2018948,SRX2018949,SRX2018950,SRX2018954,SRX2018957,SRX2018966,SRX2018967,SRX2018970,SRX2018971,SRX2018972## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 37 variables:
## ..$ SRR4026967: int [1:58302] 0 1 0 2 0 0 0 0 0 0 ...
## ..$ SRR4026968: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026969: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026970: int [1:58302] 2 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026971: int [1:58302] 0 0 0 0 0 0 0 0 0 3 ...
## ..$ SRR4026973: int [1:58302] 1 2 0 0 0 0 0 0 0 2 ...
## ..$ SRR4026974: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026976: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026977: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026979: int [1:58302] 0 5 0 0 0 0 0 0 0 2 ...
## ..$ SRR4026981: int [1:58302] 0 4 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026982: int [1:58302] 1 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026983: int [1:58302] 0 4 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026985: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026987: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026989: int [1:58302] 2 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026990: int [1:58302] 0 2 0 0 0 0 0 0 0 2 ...
## ..$ SRR4026991: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026992: int [1:58302] 1 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR4026993: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026994: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026995: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026997: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026998: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR4027000: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027001: int [1:58302] 1 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027005: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027006: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027009: int [1:58302] 1 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027010: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027012: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027013: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027014: int [1:58302] 1 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR4027015: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027017: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027018: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027019: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 37 variables:
## ..$ SRR4026967: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026968: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026969: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026970: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026971: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026973: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026974: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026976: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026977: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026982: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026983: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026985: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026987: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026989: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026990: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026991: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026992: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026993: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026994: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026995: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026997: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026998: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027000: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027001: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027005: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027006: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027009: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027010: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027012: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027013: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027014: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027015: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027017: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027018: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4027019: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 37 variables:
## ..$ SRR4026967: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026968: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026969: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026970: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026971: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026973: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026974: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026976: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026977: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026979: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026981: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026982: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026983: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026985: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026987: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026989: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026990: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026991: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026992: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026993: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026994: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026995: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026997: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4026998: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027000: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027001: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027005: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027006: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027009: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027010: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027012: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027013: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027014: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027015: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027017: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027018: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR4027019: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 37 obs. of 7 variables:
## ..$ QC_summary : chr [1:37] "WARN(5)" "WARN(5,7)" "WARN(5,8)" "WARN(5)" ...
## ..$ SRX_accession: chr [1:37] "SRX2018924" "SRX2018925" "SRX2018926" "SRX2018927" ...
## ..$ SRS_accession: chr [1:37] "SRS1614777" "SRS1614778" "SRS1614779" "SRS1614780" ...
## ..$ SRP_accession: chr [1:37] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:37] "GSM2275115" "GSM2275116" "GSM2275117" "GSM2275118" ...
## ..$ GEO_series : chr [1:37] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:37] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 37 obs. of 52 variables:
## ..$ QC_summary : chr [1:37] "WARN(5)" "WARN(5,7)" "WARN(5,8)" "WARN(5)" ...
## ..$ SRX_accession : chr [1:37] "SRX2018924" "SRX2018925" "SRX2018926" "SRX2018927" ...
## ..$ SRS_accession : chr [1:37] "SRS1614777" "SRS1614778" "SRS1614779" "SRS1614780" ...
## ..$ SRP_accession : chr [1:37] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ Sample_name : chr [1:37] "GSM2275115" "GSM2275116" "GSM2275117" "GSM2275118" ...
## ..$ GEO_series : chr [1:37] "GSE85531" "GSE85531" "GSE85531" "GSE85531" ...
## ..$ Library_name : logi [1:37] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:37] "GSM2275115" "GSM2275116" "GSM2275117" "GSM2275118" ...
## ..$ ReleaseDate : chr [1:37] "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" "2016-11-21 10:14:45" ...
## ..$ LoadDate : chr [1:37] "2016-08-12 18:08:03" "2016-08-12 18:07:39" "2016-08-12 18:07:48" "2016-08-12 18:07:58" ...
## ..$ spots : int [1:37] 13229876 10663541 11563845 12680301 12376291 13355440 10942190 11268443 12248776 11505927 ...
## ..$ bases : int [1:37] 661493800 533177050 578192250 634015050 618814550 667772000 547109500 563422150 612438800 575296350 ...
## ..$ spots_with_mates : int [1:37] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:37] 50 50 50 50 50 50 50 50 50 50 ...
## ..$ size_MB : int [1:37] 417 336 364 400 387 423 343 354 387 364 ...
## ..$ AssemblyName : logi [1:37] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:37] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026967/SRR4026967.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026968/SRR4026968.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026969/SRR4026969.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026970/SRR4026970.1" ...
## ..$ LibraryName : logi [1:37] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:37] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:37] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:37] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:37] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:37] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:37] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:37] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:37] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:37] "SRP081605" "SRP081605" "SRP081605" "SRP081605" ...
## ..$ BioProject : chr [1:37] "PRJNA338797" "PRJNA338797" "PRJNA338797" "PRJNA338797" ...
## ..$ Study_Pubmed_id : logi [1:37] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:37] 338797 338797 338797 338797 338797 338797 338797 338797 338797 338797 ...
## ..$ Sample : chr [1:37] "SRS1614777" "SRS1614778" "SRS1614779" "SRS1614780" ...
## ..$ BioSample : chr [1:37] "SAMN05570761" "SAMN05570760" "SAMN05570759" "SAMN05570758" ...
## ..$ SampleType : chr [1:37] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:37] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:37] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:37] NA NA NA NA NA NA ...
## ..$ source : logi [1:37] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:37] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:37] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:37] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:37] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:37] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:37] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:37] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:37] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:37] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:37] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:37] "SRA452046" "SRA452046" "SRA452046" "SRA452046" ...
## ..$ dbgap_study_accession: logi [1:37] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:37] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:37] "0EC164F8786F8A81BA54A847C4482163" "155BCCDBAF050DA8DB026ED80518287C" "BCD98D8A8A2F8F99CBB176EF2836DA8F" "68D131D31C0C1CC22F4C17EADC90C27E" ...
## ..$ ReadHash : chr [1:37] "665464FDC987222004CECFF6DE33564D" "A9B3EA7AD945DD71CDC607AB42656577" "2304249FDCCC9EE39CD0C07A7FAA7F06" "FCED9D0D47C63FBE4A4EABEB2D845CED" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 81 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP090853: Genes expressed differentially regulated in cancer cells by the suppression of mNT:Ctrl; SRX2210964,SRX2210965,SRX2210966:mNTsupres;SRX2210967,SRX2210968,SRX2210969## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR4344137: int [1:58302] 1 13 1 0 0 0 0 0 0 0 ...
## ..$ SRR4344138: int [1:58302] 1 27 3 0 0 0 0 0 0 0 ...
## ..$ SRR4344139: int [1:58302] 1 16 1 0 0 0 0 0 0 0 ...
## ..$ SRR4344140: int [1:58302] 0 31 2 0 0 0 0 0 0 0 ...
## ..$ SRR4344141: int [1:58302] 1 21 4 1 0 0 0 0 0 0 ...
## ..$ SRR4344142: int [1:58302] 1 4 2 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR4344137: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4344138: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4344139: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4344140: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4344141: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4344142: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR4344137: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4344138: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4344139: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4344140: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4344141: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR4344142: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX2210964" "SRX2210965" "SRX2210966" "SRX2210967" ...
## ..$ SRS_accession: chr [1:6] "SRS1728095" "SRS1728096" "SRS1728097" "SRS1728098" ...
## ..$ SRP_accession: chr [1:6] "SRP090853" "SRP090853" "SRP090853" "SRP090853" ...
## ..$ Sample_name : chr [1:6] "GSM2335754" "GSM2335755" "GSM2335756" "GSM2335757" ...
## ..$ GEO_series : chr [1:6] "GSE87626" "GSE87626" "GSE87626" "GSE87626" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX2210964" "SRX2210965" "SRX2210966" "SRX2210967" ...
## ..$ SRS_accession : chr [1:6] "SRS1728095" "SRS1728096" "SRS1728097" "SRS1728098" ...
## ..$ SRP_accession : chr [1:6] "SRP090853" "SRP090853" "SRP090853" "SRP090853" ...
## ..$ Sample_name : chr [1:6] "GSM2335754" "GSM2335755" "GSM2335756" "GSM2335757" ...
## ..$ GEO_series : chr [1:6] "GSE87626" "GSE87626" "GSE87626" "GSE87626" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2335754" "GSM2335755" "GSM2335756" "GSM2335757" ...
## ..$ ReleaseDate : chr [1:6] "2017-03-25 16:53:10" "2017-03-25 16:53:10" "2017-03-25 16:53:10" "2017-03-25 16:53:10" ...
## ..$ LoadDate : chr [1:6] "2016-10-05 08:28:55" "2016-10-05 08:42:33" "2016-10-05 08:31:28" "2016-10-05 08:28:05" ...
## ..$ spots : int [1:6] 17920510 27402210 17961877 24443413 19161290 10600499
## ..$ bases : num [1:6] 3.62e+09 5.54e+09 3.63e+09 4.94e+09 3.87e+09 ...
## ..$ spots_with_mates : int [1:6] 17920510 27402210 17961877 24443413 19161290 10600499
## ..$ avgLength : int [1:6] 202 202 202 202 202 202
## ..$ size_MB : int [1:6] 2391 3662 2399 3273 2572 1421
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4344137/SRR4344137.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR4344138/SRR4344138.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR4344139/SRR4344139.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4344140/SRR4344140.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP090853" "SRP090853" "SRP090853" "SRP090853" ...
## ..$ BioProject : chr [1:6] "PRJNA345431" "PRJNA345431" "PRJNA345431" "PRJNA345431" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 345431 345431 345431 345431 345431 345431
## ..$ Sample : chr [1:6] "SRS1728095" "SRS1728096" "SRS1728097" "SRS1728098" ...
## ..$ BioSample : chr [1:6] "SAMN05862247" "SAMN05862252" "SAMN05862251" "SAMN05862250" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA481948" "SRA481948" "SRA481948" "SRA481948" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "CB2F33502BCBFE80A7A3FA548AB29599" "1EB693D3930F86A9C40C88D058984408" "5159CFF4B4F62AEFAC3365AA0282A371" "41602A3DC93A503E79F7EA2A7B795474" ...
## ..$ ReadHash : chr [1:6] "EF746BEABA8C33482F8A3E47DB4D92BF" "58BB41D175380F9C5D4FF2BCED3DBDF8" "DA4074B8E11CE608BB62F672D42A27C8" "6E4FEDB03267994876A34F459F8A408E" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP102710: Genes expressed differentially in brown adipose tissue vs omental fat:BAT; SRX2683725,SRX2683726,SRX2683727,SRX2683728:OME; SRX2683729,SRX2683730,SRX2683731## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 7 variables:
## ..$ SRR5388839: int [1:58302] 0 64 13 0 0 0 0 2 0 0 ...
## ..$ SRR5388840: int [1:58302] 0 200 19 0 0 0 0 0 0 3 ...
## ..$ SRR5388841: int [1:58302] 0 86 5 0 0 0 0 0 0 0 ...
## ..$ SRR5388842: int [1:58302] 1 211 24 0 0 1 0 0 0 0 ...
## ..$ SRR5388843: int [1:58302] 0 111 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388844: int [1:58302] 0 79 1 0 0 0 0 0 0 0 ...
## ..$ SRR5388845: int [1:58302] 0 32 2 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 7 variables:
## ..$ SRR5388839: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388840: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388841: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388842: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388843: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388844: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388845: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 7 variables:
## ..$ SRR5388839: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388840: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388841: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388842: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388843: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388844: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388845: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 7 obs. of 7 variables:
## ..$ QC_summary : chr [1:7] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:7] "SRX2683725" "SRX2683726" "SRX2683727" "SRX2683728" ...
## ..$ SRS_accession: chr [1:7] "SRS2080932" "SRS2080933" "SRS2080936" "SRS2080934" ...
## ..$ SRP_accession: chr [1:7] "SRP102710" "SRP102710" "SRP102710" "SRP102710" ...
## ..$ Sample_name : chr [1:7] "GSM2559639" "GSM2559640" "GSM2559641" "GSM2559642" ...
## ..$ GEO_series : chr [1:7] "GSE97205" "GSE97205" "GSE97205" "GSE97205" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 7 obs. of 52 variables:
## ..$ QC_summary : chr [1:7] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:7] "SRX2683725" "SRX2683726" "SRX2683727" "SRX2683728" ...
## ..$ SRS_accession : chr [1:7] "SRS2080932" "SRS2080933" "SRS2080936" "SRS2080934" ...
## ..$ SRP_accession : chr [1:7] "SRP102710" "SRP102710" "SRP102710" "SRP102710" ...
## ..$ Sample_name : chr [1:7] "GSM2559639" "GSM2559640" "GSM2559641" "GSM2559642" ...
## ..$ GEO_series : chr [1:7] "GSE97205" "GSE97205" "GSE97205" "GSE97205" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:7] "GSM2559639" "GSM2559640" "GSM2559641" "GSM2559642" ...
## ..$ ReleaseDate : chr [1:7] "2018-04-16 16:01:33" "2018-04-16 16:01:33" "2018-04-16 16:01:33" "2018-04-16 16:01:33" ...
## ..$ LoadDate : chr [1:7] "2017-04-14 06:52:36" "2017-04-14 06:55:16" "2017-04-14 06:50:33" "2017-04-14 06:52:17" ...
## ..$ spots : int [1:7] 41650497 43541914 42668299 41003857 33092478 34350554 30126048
## ..$ bases : num [1:7] 8.33e+09 8.71e+09 8.53e+09 8.20e+09 6.62e+09 ...
## ..$ spots_with_mates : int [1:7] 41650497 43541914 42668299 41003857 33092478 34350554 30126048
## ..$ avgLength : int [1:7] 200 200 200 200 200 200 200
## ..$ size_MB : int [1:7] 4890 5132 5020 4813 3948 4078 3581
## ..$ AssemblyName : logi [1:7] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:7] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388839/SRR5388839.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388840/SRR5388840.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388841/SRR5388841.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388842/SRR5388842.1" ...
## ..$ LibraryName : logi [1:7] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:7] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:7] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:7] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:7] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:7] 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:7] 0 0 0 0 0 0 0
## ..$ Platform : chr [1:7] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:7] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:7] "SRP102710" "SRP102710" "SRP102710" "SRP102710" ...
## ..$ BioProject : chr [1:7] "PRJNA380957" "PRJNA380957" "PRJNA380957" "PRJNA380957" ...
## ..$ Study_Pubmed_id : int [1:7] 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:7] 380957 380957 380957 380957 380957 380957 380957
## ..$ Sample : chr [1:7] "SRS2080932" "SRS2080933" "SRS2080936" "SRS2080934" ...
## ..$ BioSample : chr [1:7] "SAMN06652341" "SAMN06652340" "SAMN06652339" "SAMN06652338" ...
## ..$ SampleType : chr [1:7] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:7] 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:7] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:7] NA NA NA NA NA NA ...
## ..$ source : logi [1:7] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:7] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:7] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:7] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:7] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:7] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:7] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:7] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:7] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:7] "SRA550348" "SRA550348" "SRA550348" "SRA550348" ...
## ..$ dbgap_study_accession: logi [1:7] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:7] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:7] "AEC6E4E8BE87763C6EF8369D58CC6187" "6911E65550F33960B83C1B26A12D833F" "A167B644C035D8E520BF4B86464DE17B" "B90334596E075F26DA000F08B13428D3" ...
## ..$ ReadHash : chr [1:7] "A73EDA1EFD0098D18D82775A6DAFE928" "DE6F38AC07C6144688C59B28E2B0C527" "AC10B6F2019ED70BAA4B21EEF8EABC54" "1A325707B8188E59B019C559C83F2E65" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP102710: Genes expressed differentially in brown adipose tissue vs subcutaneous fat:BAT;SRX2683725,SRX2683726,SRX2683727,SRX2683728:SUB; SRX2683732,SRX2683733,SRX2683734## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 7 variables:
## ..$ SRR5388839: int [1:58302] 0 64 13 0 0 0 0 2 0 0 ...
## ..$ SRR5388840: int [1:58302] 0 200 19 0 0 0 0 0 0 3 ...
## ..$ SRR5388841: int [1:58302] 0 86 5 0 0 0 0 0 0 0 ...
## ..$ SRR5388842: int [1:58302] 1 211 24 0 0 1 0 0 0 0 ...
## ..$ SRR5388846: int [1:58302] 0 33 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388847: int [1:58302] 0 82 0 0 0 0 0 0 0 19 ...
## ..$ SRR5388848: int [1:58302] 0 49 5 1 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 7 variables:
## ..$ SRR5388839: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388840: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388841: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388842: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388846: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388847: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388848: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 7 variables:
## ..$ SRR5388839: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388840: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388841: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388842: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388846: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388847: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388848: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 7 obs. of 7 variables:
## ..$ QC_summary : chr [1:7] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:7] "SRX2683725" "SRX2683726" "SRX2683727" "SRX2683728" ...
## ..$ SRS_accession: chr [1:7] "SRS2080932" "SRS2080933" "SRS2080936" "SRS2080934" ...
## ..$ SRP_accession: chr [1:7] "SRP102710" "SRP102710" "SRP102710" "SRP102710" ...
## ..$ Sample_name : chr [1:7] "GSM2559639" "GSM2559640" "GSM2559641" "GSM2559642" ...
## ..$ GEO_series : chr [1:7] "GSE97205" "GSE97205" "GSE97205" "GSE97205" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 7 obs. of 52 variables:
## ..$ QC_summary : chr [1:7] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:7] "SRX2683725" "SRX2683726" "SRX2683727" "SRX2683728" ...
## ..$ SRS_accession : chr [1:7] "SRS2080932" "SRS2080933" "SRS2080936" "SRS2080934" ...
## ..$ SRP_accession : chr [1:7] "SRP102710" "SRP102710" "SRP102710" "SRP102710" ...
## ..$ Sample_name : chr [1:7] "GSM2559639" "GSM2559640" "GSM2559641" "GSM2559642" ...
## ..$ GEO_series : chr [1:7] "GSE97205" "GSE97205" "GSE97205" "GSE97205" ...
## ..$ Library_name : logi [1:7] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:7] "GSM2559639" "GSM2559640" "GSM2559641" "GSM2559642" ...
## ..$ ReleaseDate : chr [1:7] "2018-04-16 16:01:33" "2018-04-16 16:01:33" "2018-04-16 16:01:33" "2018-04-16 16:01:33" ...
## ..$ LoadDate : chr [1:7] "2017-04-14 06:52:36" "2017-04-14 06:55:16" "2017-04-14 06:50:33" "2017-04-14 06:52:17" ...
## ..$ spots : int [1:7] 41650497 43541914 42668299 41003857 29707450 26788932 23653371
## ..$ bases : num [1:7] 8.33e+09 8.71e+09 8.53e+09 8.20e+09 5.94e+09 ...
## ..$ spots_with_mates : int [1:7] 41650497 43541914 42668299 41003857 29707450 26788932 23653371
## ..$ avgLength : int [1:7] 200 200 200 200 200 200 200
## ..$ size_MB : int [1:7] 4890 5132 5020 4813 3538 3171 2794
## ..$ AssemblyName : logi [1:7] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:7] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388839/SRR5388839.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388840/SRR5388840.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388841/SRR5388841.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388842/SRR5388842.1" ...
## ..$ LibraryName : logi [1:7] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:7] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:7] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:7] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:7] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:7] 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:7] 0 0 0 0 0 0 0
## ..$ Platform : chr [1:7] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:7] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:7] "SRP102710" "SRP102710" "SRP102710" "SRP102710" ...
## ..$ BioProject : chr [1:7] "PRJNA380957" "PRJNA380957" "PRJNA380957" "PRJNA380957" ...
## ..$ Study_Pubmed_id : int [1:7] 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:7] 380957 380957 380957 380957 380957 380957 380957
## ..$ Sample : chr [1:7] "SRS2080932" "SRS2080933" "SRS2080936" "SRS2080934" ...
## ..$ BioSample : chr [1:7] "SAMN06652341" "SAMN06652340" "SAMN06652339" "SAMN06652338" ...
## ..$ SampleType : chr [1:7] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:7] 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:7] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:7] NA NA NA NA NA NA ...
## ..$ source : logi [1:7] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:7] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:7] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:7] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:7] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:7] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:7] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:7] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:7] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:7] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:7] "SRA550348" "SRA550348" "SRA550348" "SRA550348" ...
## ..$ dbgap_study_accession: logi [1:7] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:7] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:7] "AEC6E4E8BE87763C6EF8369D58CC6187" "6911E65550F33960B83C1B26A12D833F" "A167B644C035D8E520BF4B86464DE17B" "B90334596E075F26DA000F08B13428D3" ...
## ..$ ReadHash : chr [1:7] "A73EDA1EFD0098D18D82775A6DAFE928" "DE6F38AC07C6144688C59B28E2B0C527" "AC10B6F2019ED70BAA4B21EEF8EABC54" "1A325707B8188E59B019C559C83F2E65" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP102710: Genes expressed differentially in omental fat vs subcutaneous fat:OME; SRX2683729,SRX2683730,SRX2683731:SUB; SRX2683732,SRX2683733,SRX2683734## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR5388843: int [1:58302] 0 111 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388844: int [1:58302] 0 79 1 0 0 0 0 0 0 0 ...
## ..$ SRR5388845: int [1:58302] 0 32 2 0 0 0 0 0 0 1 ...
## ..$ SRR5388846: int [1:58302] 0 33 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388847: int [1:58302] 0 82 0 0 0 0 0 0 0 19 ...
## ..$ SRR5388848: int [1:58302] 0 49 5 1 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR5388843: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388844: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388845: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388846: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388847: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5388848: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR5388843: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388844: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388845: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388846: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388847: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5388848: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX2683729" "SRX2683730" "SRX2683731" "SRX2683732" ...
## ..$ SRS_accession: chr [1:6] "SRS2080935" "SRS2080937" "SRS2080938" "SRS2080939" ...
## ..$ SRP_accession: chr [1:6] "SRP102710" "SRP102710" "SRP102710" "SRP102710" ...
## ..$ Sample_name : chr [1:6] "GSM2559643" "GSM2559644" "GSM2559645" "GSM2559646" ...
## ..$ GEO_series : chr [1:6] "GSE97205" "GSE97205" "GSE97205" "GSE97205" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX2683729" "SRX2683730" "SRX2683731" "SRX2683732" ...
## ..$ SRS_accession : chr [1:6] "SRS2080935" "SRS2080937" "SRS2080938" "SRS2080939" ...
## ..$ SRP_accession : chr [1:6] "SRP102710" "SRP102710" "SRP102710" "SRP102710" ...
## ..$ Sample_name : chr [1:6] "GSM2559643" "GSM2559644" "GSM2559645" "GSM2559646" ...
## ..$ GEO_series : chr [1:6] "GSE97205" "GSE97205" "GSE97205" "GSE97205" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2559643" "GSM2559644" "GSM2559645" "GSM2559646" ...
## ..$ ReleaseDate : chr [1:6] "2018-04-16 16:01:33" "2018-04-16 16:01:33" "2018-04-16 16:01:33" "2018-04-16 16:01:33" ...
## ..$ LoadDate : chr [1:6] "2017-04-14 06:46:38" "2017-04-14 06:47:43" "2017-04-14 06:47:13" "2017-04-14 06:45:52" ...
## ..$ spots : int [1:6] 33092478 34350554 30126048 29707450 26788932 23653371
## ..$ bases : num [1:6] 6.62e+09 6.87e+09 6.03e+09 5.94e+09 5.36e+09 ...
## ..$ spots_with_mates : int [1:6] 33092478 34350554 30126048 29707450 26788932 23653371
## ..$ avgLength : int [1:6] 200 200 200 200 200 200
## ..$ size_MB : int [1:6] 3948 4078 3581 3538 3171 2794
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388843/SRR5388843.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388844/SRR5388844.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388845/SRR5388845.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5388846/SRR5388846.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP102710" "SRP102710" "SRP102710" "SRP102710" ...
## ..$ BioProject : chr [1:6] "PRJNA380957" "PRJNA380957" "PRJNA380957" "PRJNA380957" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 380957 380957 380957 380957 380957 380957
## ..$ Sample : chr [1:6] "SRS2080935" "SRS2080937" "SRS2080938" "SRS2080939" ...
## ..$ BioSample : chr [1:6] "SAMN06652337" "SAMN06652327" "SAMN06652336" "SAMN06652335" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA550348" "SRA550348" "SRA550348" "SRA550348" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "6CF802400B92E57AD3F8D6521F117AEF" "0B9282056C7C419B1A739D9AE806EA3C" "FBBF14E02A2D03643FBD21A15C2809A2" "D8D98FAB24525E983A8E429A3705F0CE" ...
## ..$ ReadHash : chr [1:6] "0A10FCF51D9E9B9A4DE4EBE6BC0B9892" "474ED9B4D36EBF93B2AC3F72E2614F04" "DCB4AA21A7190F381963B86FBC3BAABB" "CA1722DC1A2891F7AFD6E5CD8610BC48" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP095538: Genes expressed differentially in glucose tolerant vs gestational diabetes sncRNA-Seq:Ctrl;SRX2440262,SRX2440264,SRX2440266,SRX2440268,SRX2440270,SRX2440272,SRX2440274,SRX2440276:GDM; SRX2440263,SRX2440265,SRX2440267,SRX2440269,SRX2440271,SRX2440273,SRX2440275,SRX2440277## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 16 variables:
## ..$ SRR5125872: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125873: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125874: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125875: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125876: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125877: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125878: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125879: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125880: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125881: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125882: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125883: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125884: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125885: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125886: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125887: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 16 variables:
## ..$ SRR5125872: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125873: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125874: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125875: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125876: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125877: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125878: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125879: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125880: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125881: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125882: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125883: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125884: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125885: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125886: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125887: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 16 variables:
## ..$ SRR5125872: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125873: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125874: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125875: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125876: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125877: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125878: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125879: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125880: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125881: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125882: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125883: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125884: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125885: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125886: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5125887: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 16 obs. of 7 variables:
## ..$ QC_summary : chr [1:16] "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(4,6,7)" ...
## ..$ SRX_accession: chr [1:16] "SRX2440262" "SRX2440263" "SRX2440264" "SRX2440265" ...
## ..$ SRS_accession: chr [1:16] "SRS1874849" "SRS1874850" "SRS1874851" "SRS1874852" ...
## ..$ SRP_accession: chr [1:16] "SRP095538" "SRP095538" "SRP095538" "SRP095538" ...
## ..$ Sample_name : chr [1:16] "GSM2437162" "GSM2437163" "GSM2437164" "GSM2437165" ...
## ..$ GEO_series : chr [1:16] "GSE92772" "GSE92772" "GSE92772" "GSE92772" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 16 obs. of 52 variables:
## ..$ QC_summary : chr [1:16] "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(4,6,7)" ...
## ..$ SRX_accession : chr [1:16] "SRX2440262" "SRX2440263" "SRX2440264" "SRX2440265" ...
## ..$ SRS_accession : chr [1:16] "SRS1874849" "SRS1874850" "SRS1874851" "SRS1874852" ...
## ..$ SRP_accession : chr [1:16] "SRP095538" "SRP095538" "SRP095538" "SRP095538" ...
## ..$ Sample_name : chr [1:16] "GSM2437162" "GSM2437163" "GSM2437164" "GSM2437165" ...
## ..$ GEO_series : chr [1:16] "GSE92772" "GSE92772" "GSE92772" "GSE92772" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:16] "GSM2437162" "GSM2437163" "GSM2437164" "GSM2437165" ...
## ..$ ReleaseDate : chr [1:16] "2018-01-02 09:22:04" "2018-01-02 09:22:04" "2018-01-02 09:22:04" "2018-01-02 09:22:04" ...
## ..$ LoadDate : chr [1:16] "2016-12-22 13:47:44" "2016-12-22 13:48:25" "2016-12-22 13:48:04" "2016-12-22 13:47:58" ...
## ..$ spots : int [1:16] 16797990 17254961 17079021 16022543 18058519 16695371 17045263 17066693 15696060 17592017 ...
## ..$ bases : int [1:16] 856697490 880003011 871030071 817149693 920984469 851463921 869308413 870401343 800499060 897192867 ...
## ..$ spots_with_mates : int [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:16] 51 51 51 51 51 51 51 51 51 51 ...
## ..$ size_MB : int [1:16] 355 360 359 334 378 351 354 358 333 371 ...
## ..$ AssemblyName : logi [1:16] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:16] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125872/SRR5125872.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125873/SRR5125873.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125874/SRR5125874.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125875/SRR5125875.1" ...
## ..$ LibraryName : logi [1:16] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:16] "ncRNA-Seq" "ncRNA-Seq" "ncRNA-Seq" "ncRNA-Seq" ...
## ..$ LibrarySelection : chr [1:16] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ LibrarySource : chr [1:16] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:16] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:16] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:16] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:16] "SRP095538" "SRP095538" "SRP095538" "SRP095538" ...
## ..$ BioProject : chr [1:16] "PRJNA358580" "PRJNA358580" "PRJNA358580" "PRJNA358580" ...
## ..$ Study_Pubmed_id : int [1:16] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:16] 358580 358580 358580 358580 358580 358580 358580 358580 358580 358580 ...
## ..$ Sample : chr [1:16] "SRS1874849" "SRS1874850" "SRS1874851" "SRS1874852" ...
## ..$ BioSample : chr [1:16] "SAMN06175187" "SAMN06175186" "SAMN06175185" "SAMN06175184" ...
## ..$ SampleType : chr [1:16] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:16] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:16] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:16] NA NA NA NA NA NA ...
## ..$ source : logi [1:16] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:16] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:16] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:16] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:16] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:16] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:16] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:16] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:16] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:16] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:16] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:16] "SRA508060" "SRA508060" "SRA508060" "SRA508060" ...
## ..$ dbgap_study_accession: logi [1:16] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:16] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:16] "460864F05C48B97ACA830B93C57DB263" "35043C3F46644137C3DD70B627B4F1B9" "E6020E1D76C3E57DB40C10757959025B" "B1D9AEF6AD9A3819A8AAB99ADD0E5C32" ...
## ..$ ReadHash : chr [1:16] "F6F6A2CDD9DE1718545BAF143A23B2D7" "77AE84D71FAA319832D1CC3C45BFDAEE" "0F7A4095C656F848EB7EA3C77B440B2A" "BDE8CF0AAC368A19ABEDF87F73ADCAF4" ...
## $ absent : chr(0)## SRP095538: Genes expressed differentially in glucose tolerant vs gestational diabetes RNA-Seq:Ctrl; SRX2440278,SRX2440280,SRX2440282,SRX2440284,SRX2440286,SRX2440288,SRX2440290,SRX2440292:GDM; SRX2440279,SRX2440281,SRX2440283,SRX2440285,SRX2440287,SRX2440289,SRX2440291,SRX2440293
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 13 variables:
## ..$ SRR5125888: int [1:58302] 2 36 0 0 0 0 0 0 1 62 ...
## ..$ SRR5125891: int [1:58302] 5 9 0 0 0 0 0 0 0 25 ...
## ..$ SRR5125892: int [1:58302] 2 11 1 0 0 0 3 0 0 73 ...
## ..$ SRR5125893: int [1:58302] 0 9 2 0 0 0 1 0 0 68 ...
## ..$ SRR5125894: int [1:58302] 2 16 2 0 0 0 0 0 0 30 ...
## ..$ SRR5125895: int [1:58302] 1 10 0 0 0 0 0 0 0 23 ...
## ..$ SRR5125896: int [1:58302] 0 27 0 0 0 0 0 0 0 46 ...
## ..$ SRR5125897: int [1:58302] 2 20 0 0 0 0 0 0 0 108 ...
## ..$ SRR5125898: int [1:58302] 2 20 0 0 0 0 0 0 0 8 ...
## ..$ SRR5125899: int [1:58302] 45 83 0 0 0 0 42 0 0 30 ...
## ..$ SRR5125900: int [1:58302] 0 14 3 0 0 0 0 0 0 34 ...
## ..$ SRR5125902: int [1:58302] 1 47 0 0 0 0 0 0 0 51 ...
## ..$ SRR5125903: int [1:58302] 0 7 0 0 0 0 0 0 0 33 ...
## $ TxCounts :'data.frame': 180869 obs. of 13 variables:
## ..$ SRR5125888: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125891: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125892: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125893: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125894: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125895: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125896: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125897: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125898: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125899: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125900: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125902: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125903: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 13 variables:
## ..$ SRR5125888: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125891: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125892: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125893: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125894: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125895: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125896: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125897: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125898: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125899: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125900: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125902: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5125903: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 13 obs. of 7 variables:
## ..$ QC_summary : chr [1:13] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(2)" ...
## ..$ SRX_accession: chr [1:13] "SRX2440278" "SRX2440281" "SRX2440282" "SRX2440283" ...
## ..$ SRS_accession: chr [1:13] "SRS1874865" "SRS1874868" "SRS1874869" "SRS1874870" ...
## ..$ SRP_accession: chr [1:13] "SRP095538" "SRP095538" "SRP095538" "SRP095538" ...
## ..$ Sample_name : chr [1:13] "GSM2437178" "GSM2437181" "GSM2437182" "GSM2437183" ...
## ..$ GEO_series : chr [1:13] "GSE92772" "GSE92772" "GSE92772" "GSE92772" ...
## ..$ Library_name : logi [1:13] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 13 obs. of 52 variables:
## ..$ QC_summary : chr [1:13] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(2)" ...
## ..$ SRX_accession : chr [1:13] "SRX2440278" "SRX2440281" "SRX2440282" "SRX2440283" ...
## ..$ SRS_accession : chr [1:13] "SRS1874865" "SRS1874868" "SRS1874869" "SRS1874870" ...
## ..$ SRP_accession : chr [1:13] "SRP095538" "SRP095538" "SRP095538" "SRP095538" ...
## ..$ Sample_name : chr [1:13] "GSM2437178" "GSM2437181" "GSM2437182" "GSM2437183" ...
## ..$ GEO_series : chr [1:13] "GSE92772" "GSE92772" "GSE92772" "GSE92772" ...
## ..$ Library_name : logi [1:13] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:13] "GSM2437178" "GSM2437181" "GSM2437182" "GSM2437183" ...
## ..$ ReleaseDate : chr [1:13] "2018-01-02 09:22:04" "2018-01-02 09:22:04" "2018-01-02 09:22:04" "2018-01-02 09:22:04" ...
## ..$ LoadDate : chr [1:13] "2016-12-22 15:02:29" "2016-12-22 15:08:20" "2016-12-22 14:51:20" "2016-12-22 14:55:58" ...
## ..$ spots : int [1:13] 104724237 99325063 93329552 96352851 92459415 98329076 89853792 112434086 98033122 90097550 ...
## ..$ bases : num [1:13] 2.12e+10 2.01e+10 1.89e+10 1.95e+10 1.87e+10 ...
## ..$ spots_with_mates : int [1:13] 104724237 99325063 93329552 96352851 92459415 98329076 89853792 112434086 98033122 90097550 ...
## ..$ avgLength : int [1:13] 202 202 202 202 202 202 202 202 202 202 ...
## ..$ size_MB : int [1:13] 9426 8872 8371 8692 8297 8883 8104 10085 8919 8150 ...
## ..$ AssemblyName : logi [1:13] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:13] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125888/SRR5125888.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125891/SRR5125891.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125892/SRR5125892.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125893/SRR5125893.1" ...
## ..$ LibraryName : logi [1:13] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:13] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:13] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:13] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:13] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:13] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:13] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:13] "SRP095538" "SRP095538" "SRP095538" "SRP095538" ...
## ..$ BioProject : chr [1:13] "PRJNA358580" "PRJNA358580" "PRJNA358580" "PRJNA358580" ...
## ..$ Study_Pubmed_id : int [1:13] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:13] 358580 358580 358580 358580 358580 358580 358580 358580 358580 358580 ...
## ..$ Sample : chr [1:13] "SRS1874865" "SRS1874868" "SRS1874869" "SRS1874870" ...
## ..$ BioSample : chr [1:13] "SAMN06175203" "SAMN06175200" "SAMN06175199" "SAMN06175198" ...
## ..$ SampleType : chr [1:13] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:13] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:13] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:13] NA NA NA NA NA NA ...
## ..$ source : logi [1:13] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:13] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:13] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:13] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:13] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:13] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:13] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:13] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:13] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:13] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:13] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:13] "SRA508060" "SRA508060" "SRA508060" "SRA508060" ...
## ..$ dbgap_study_accession: logi [1:13] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:13] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:13] "BD7E838F246223CC854DDBA8C5C232D0" "545D28F4A862C913627F1F26BF24CC31" "40F280138227A3E40FA41A65F071B223" "FA75BF29B1D911C86400001B83A49D5D" ...
## ..$ ReadHash : chr [1:13] "A52D9426D0CAA96718BC6E954C5B198E" "DF80630351AD66460C9DD7239407A74B" "693E48610C3700C9724B00A01C72E902" "86D834B77C343D31220CB9A79564E4B7" ...
## $ absent : chr(0)## SRP095512: Genes expressed differentially in health vs diabetic dermal endothelial cells:Ctrl; SRX2439830,SRX2439835,SRX2439836,SRX2439837,SRX2439838,SRX2439839:T2D; SRX2439831,SRX2439832,SRX2439833,SRX2439834
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 9 variables:
## ..$ SRR5125028: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125030: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125031: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125032: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125033: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125034: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125035: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125036: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125037: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 9 variables:
## ..$ SRR5125028: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125030: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125031: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125032: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125033: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125034: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125035: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125036: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5125037: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 9 variables:
## ..$ SRR5125028: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5125030: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5125031: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5125032: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5125033: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5125034: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5125035: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5125036: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5125037: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 9 obs. of 7 variables:
## ..$ QC_summary : chr [1:9] "WARN(8)" "PASS" "WARN(4)" "PASS" ...
## ..$ SRX_accession: chr [1:9] "SRX2439830" "SRX2439832" "SRX2439833" "SRX2439834" ...
## ..$ SRS_accession: chr [1:9] "SRS1874419" "SRS1874421" "SRS1874422" "SRS1874423" ...
## ..$ SRP_accession: chr [1:9] "SRP095512" "SRP095512" "SRP095512" "SRP095512" ...
## ..$ Sample_name : chr [1:9] "GSM2436514" "GSM2436516" "GSM2436517" "GSM2436518" ...
## ..$ GEO_series : chr [1:9] "GSE92724" "GSE92724" "GSE92724" "GSE92724" ...
## ..$ Library_name : logi [1:9] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 9 obs. of 52 variables:
## ..$ QC_summary : chr [1:9] "WARN(8)" "PASS" "WARN(4)" "PASS" ...
## ..$ SRX_accession : chr [1:9] "SRX2439830" "SRX2439832" "SRX2439833" "SRX2439834" ...
## ..$ SRS_accession : chr [1:9] "SRS1874419" "SRS1874421" "SRS1874422" "SRS1874423" ...
## ..$ SRP_accession : chr [1:9] "SRP095512" "SRP095512" "SRP095512" "SRP095512" ...
## ..$ Sample_name : chr [1:9] "GSM2436514" "GSM2436516" "GSM2436517" "GSM2436518" ...
## ..$ GEO_series : chr [1:9] "GSE92724" "GSE92724" "GSE92724" "GSE92724" ...
## ..$ Library_name : logi [1:9] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:9] "GSM2436514" "GSM2436516" "GSM2436517" "GSM2436518" ...
## ..$ ReleaseDate : chr [1:9] "2018-01-08 14:13:15" "2018-01-08 14:13:15" "2018-01-08 14:13:15" "2018-01-08 14:13:15" ...
## ..$ LoadDate : chr [1:9] "2016-12-22 07:35:30" "2016-12-22 07:35:59" "2016-12-22 07:35:27" "2016-12-22 07:35:48" ...
## ..$ spots : int [1:9] 19666725 23275350 18919646 20306155 21639627 20344890 20269745 20994615 19678781
## ..$ bases : int [1:9] 983336250 1163767500 945982300 1015307750 1081981350 1017244500 1013487250 1049730750 983939050
## ..$ spots_with_mates : int [1:9] 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:9] 50 50 50 50 50 50 50 50 50
## ..$ size_MB : int [1:9] 326 385 313 336 356 335 334 344 324
## ..$ AssemblyName : logi [1:9] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:9] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125028/SRR5125028.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125030/SRR5125030.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125031/SRR5125031.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5125032/SRR5125032.1" ...
## ..$ LibraryName : logi [1:9] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:9] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:9] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:9] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:9] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:9] 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:9] 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:9] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:9] "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" "Illumina HiSeq 4000" ...
## ..$ SRAStudy : chr [1:9] "SRP095512" "SRP095512" "SRP095512" "SRP095512" ...
## ..$ BioProject : chr [1:9] "PRJNA358470" "PRJNA358470" "PRJNA358470" "PRJNA358470" ...
## ..$ Study_Pubmed_id : int [1:9] 3 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:9] 358470 358470 358470 358470 358470 358470 358470 358470 358470
## ..$ Sample : chr [1:9] "SRS1874419" "SRS1874421" "SRS1874422" "SRS1874423" ...
## ..$ BioSample : chr [1:9] "SAMN06174289" "SAMN06174297" "SAMN06174296" "SAMN06174295" ...
## ..$ SampleType : chr [1:9] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:9] 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:9] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:9] NA NA NA NA NA NA ...
## ..$ source : logi [1:9] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:9] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:9] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:9] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:9] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:9] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:9] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:9] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:9] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:9] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:9] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:9] "SRA507438" "SRA507438" "SRA507438" "SRA507438" ...
## ..$ dbgap_study_accession: logi [1:9] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:9] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:9] "54A7DD46BE6466DFBB8DC9668EC3E073" "AF9AD8C842B31BF351CF56565E6F7AB8" "799232320D9F610FD164DAF3E7BD6A58" "7F19697CE210BFE29061E68FA939E003" ...
## ..$ ReadHash : chr [1:9] "990F8ABE7FA36A55D638F91DFEBBBD4C" "AD448C0F0B7E6464B714910DA6034CE1" "706AF2BEFDBF7DFCE08BD637AE28B750" "D3945F6AC78237C93D47C6CEC2B22DA7" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP102542: Genes expressed differentially in young people who do HIIT training:Ctrl;SRX2676303,SRX2676313,SRX2676315,SRX2676327, SRX2676329,SRX2676333,SRX2676346,SRX2676352,SRX2676360,SRX2676364,SRX2676396:HIIT; SRX2676304,SRX2676314,SRX2676316,SRX2676328,SRX2676330,SRX2676334,SRX2676347,SRX2676353,SRX2676361,SRX2676365,SRX2676397## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 22 variables:
## ..$ SRR5381160: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381161: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381170: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381171: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381172: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381173: int [1:58302] 0 8 0 0 0 0 0 0 0 1 ...
## ..$ SRR5381184: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381185: int [1:58302] 1 9 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381186: int [1:58302] 0 6 0 1 0 0 0 0 0 0 ...
## ..$ SRR5381187: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381190: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381191: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381203: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381204: int [1:58302] 0 3 0 1 0 0 0 0 0 1 ...
## ..$ SRR5381209: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381210: int [1:58302] 0 8 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381217: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381218: int [1:58302] 0 9 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381221: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381222: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381253: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381254: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 22 variables:
## ..$ SRR5381160: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381161: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381170: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381171: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381172: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381173: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381184: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381185: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381186: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381187: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381190: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381191: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381203: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381204: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381209: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381210: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381217: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381218: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381221: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381222: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381253: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381254: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 22 variables:
## ..$ SRR5381160: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381161: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381170: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381171: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381172: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381173: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381184: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381185: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381186: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381187: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381190: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381191: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381203: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381204: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381209: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381210: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381217: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381218: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381221: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381222: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381253: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381254: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 22 obs. of 7 variables:
## ..$ QC_summary : chr [1:22] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:22] "SRX2676303" "SRX2676304" "SRX2676313" "SRX2676314" ...
## ..$ SRS_accession: chr [1:22] "SRS2074806" "SRS2074809" "SRS2074818" "SRS2074819" ...
## ..$ SRP_accession: chr [1:22] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:22] "GSM2551326" "GSM2551327" "GSM2551336" "GSM2551337" ...
## ..$ GEO_series : chr [1:22] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:22] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 22 obs. of 52 variables:
## ..$ QC_summary : chr [1:22] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:22] "SRX2676303" "SRX2676304" "SRX2676313" "SRX2676314" ...
## ..$ SRS_accession : chr [1:22] "SRS2074806" "SRS2074809" "SRS2074818" "SRS2074819" ...
## ..$ SRP_accession : chr [1:22] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:22] "GSM2551326" "GSM2551327" "GSM2551336" "GSM2551337" ...
## ..$ GEO_series : chr [1:22] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:22] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:22] "GSM2551326" "GSM2551327" "GSM2551336" "GSM2551337" ...
## ..$ ReleaseDate : chr [1:22] "2017-03-30 02:41:07" "2017-03-30 02:41:07" "2017-03-30 02:41:07" "2017-03-30 02:41:07" ...
## ..$ LoadDate : chr [1:22] "2017-03-27 16:34:23" "2017-03-27 16:36:34" "2017-03-27 16:38:09" "2017-03-27 16:35:34" ...
## ..$ spots : int [1:22] 13279108 22587657 21479165 13783139 21904228 20836022 24274325 28925695 32160166 20927537 ...
## ..$ bases : num [1:22] 1.35e+09 2.30e+09 2.19e+09 1.41e+09 2.23e+09 ...
## ..$ spots_with_mates : int [1:22] 13279108 22587657 21479165 13783139 21904228 20836022 24274325 28925695 32160166 20927537 ...
## ..$ avgLength : int [1:22] 102 102 102 102 102 102 102 102 102 102 ...
## ..$ size_MB : int [1:22] 844 1432 1370 881 1400 1329 1488 1773 2149 1401 ...
## ..$ AssemblyName : logi [1:22] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:22] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381160/SRR5381160.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381161/SRR5381161.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381170/SRR5381170.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381171/SRR5381171.1" ...
## ..$ LibraryName : logi [1:22] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:22] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:22] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:22] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:22] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:22] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:22] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:22] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:22] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:22] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ BioProject : chr [1:22] "PRJNA380649" "PRJNA380649" "PRJNA380649" "PRJNA380649" ...
## ..$ Study_Pubmed_id : int [1:22] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:22] 380649 380649 380649 380649 380649 380649 380649 380649 380649 380649 ...
## ..$ Sample : chr [1:22] "SRS2074806" "SRS2074809" "SRS2074818" "SRS2074819" ...
## ..$ BioSample : chr [1:22] "SAMN06645549" "SAMN06645548" "SAMN06645539" "SAMN06645538" ...
## ..$ SampleType : chr [1:22] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:22] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:22] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:22] NA NA NA NA NA NA ...
## ..$ source : logi [1:22] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:22] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:22] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:22] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:22] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:22] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:22] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:22] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:22] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:22] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:22] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:22] "SRA549619" "SRA549619" "SRA549619" "SRA549619" ...
## ..$ dbgap_study_accession: logi [1:22] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:22] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:22] "6CFA70F4925CD880C1198D394BB6C082" "D11900144D729B68528446E04547F17D" "44F86CFBB2C939C7E8B410C6C5F91E91" "1228E38655984CCA406DDB456C192197" ...
## ..$ ReadHash : chr [1:22] "7035A14F731B6DCCDD8B61BDB06E93BA" "9DB5D7FC79F931974CD90CF05CA21997" "542E0246D9B3A182AACA0AFF2B68A9DC" "22C688896EC5FA69C1766FC5AD85A730" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 98 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP102542: Genes expressed differentially in young people who do Resistance training:Ctrl; SRX2676305,SRX2676309,SRX2676311,SRX2676317,SRX2676331,SRX2676338,SRX2676342,SRX2676348,SRX2676358,SRX2676362:Resis;SRX2676306,SRX2676312,SRX2676310,SRX2676318,SRX2676332,SRX2676339,SRX2676343,SRX2676349,SRX2676359,SRX2676363## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 20 variables:
## ..$ SRR5381162: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381163: int [1:58302] 0 4 1 2 0 0 0 0 0 0 ...
## ..$ SRR5381166: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381167: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381168: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381169: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381174: int [1:58302] 0 10 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381175: int [1:58302] 0 5 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381188: int [1:58302] 0 7 0 1 0 0 0 0 0 0 ...
## ..$ SRR5381189: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381195: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381196: int [1:58302] 0 6 2 0 0 0 0 0 0 0 ...
## ..$ SRR5381199: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381200: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381205: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381206: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381215: int [1:58302] 0 6 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381216: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381219: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381220: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 20 variables:
## ..$ SRR5381162: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381163: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381166: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381167: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381168: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381169: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381174: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381175: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381188: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381189: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381195: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381196: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381199: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381200: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381205: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381206: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381215: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381216: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381219: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381220: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 20 variables:
## ..$ SRR5381162: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381163: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381166: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381167: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381168: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381169: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381174: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381175: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381188: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381189: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381195: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381196: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381199: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381200: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381205: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381206: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381215: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381216: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381219: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381220: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 20 obs. of 7 variables:
## ..$ QC_summary : chr [1:20] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:20] "SRX2676305" "SRX2676306" "SRX2676309" "SRX2676310" ...
## ..$ SRS_accession: chr [1:20] "SRS2074810" "SRS2074811" "SRS2074814" "SRS2074816" ...
## ..$ SRP_accession: chr [1:20] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:20] "GSM2551328" "GSM2551329" "GSM2551332" "GSM2551333" ...
## ..$ GEO_series : chr [1:20] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:20] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 20 obs. of 52 variables:
## ..$ QC_summary : chr [1:20] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:20] "SRX2676305" "SRX2676306" "SRX2676309" "SRX2676310" ...
## ..$ SRS_accession : chr [1:20] "SRS2074810" "SRS2074811" "SRS2074814" "SRS2074816" ...
## ..$ SRP_accession : chr [1:20] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:20] "GSM2551328" "GSM2551329" "GSM2551332" "GSM2551333" ...
## ..$ GEO_series : chr [1:20] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:20] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:20] "GSM2551328" "GSM2551329" "GSM2551332" "GSM2551333" ...
## ..$ ReleaseDate : chr [1:20] "2017-03-30 02:41:07" "2017-03-30 02:41:07" "2017-03-30 02:41:07" "2017-03-30 02:41:07" ...
## ..$ LoadDate : chr [1:20] "2017-03-27 16:35:31" "2017-03-27 16:38:36" "2017-03-27 16:38:02" "2017-03-27 16:38:57" ...
## ..$ spots : int [1:20] 14505500 25998503 22000590 27483732 26366308 21249979 26537964 17229603 23427277 20491270 ...
## ..$ bases : num [1:20] 1.48e+09 2.65e+09 2.24e+09 2.80e+09 2.69e+09 ...
## ..$ spots_with_mates : int [1:20] 14505500 25998503 22000590 27483732 26366308 21249979 26537964 17229603 23427277 20491270 ...
## ..$ avgLength : int [1:20] 102 102 102 102 102 102 102 102 102 102 ...
## ..$ size_MB : int [1:20] 922 1644 1408 1757 1681 1356 1686 1095 1487 1304 ...
## ..$ AssemblyName : logi [1:20] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:20] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381162/SRR5381162.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381163/SRR5381163.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381166/SRR5381166.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381167/SRR5381167.1" ...
## ..$ LibraryName : logi [1:20] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:20] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:20] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:20] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:20] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:20] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:20] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:20] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:20] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:20] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ BioProject : chr [1:20] "PRJNA380649" "PRJNA380649" "PRJNA380649" "PRJNA380649" ...
## ..$ Study_Pubmed_id : int [1:20] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:20] 380649 380649 380649 380649 380649 380649 380649 380649 380649 380649 ...
## ..$ Sample : chr [1:20] "SRS2074810" "SRS2074811" "SRS2074814" "SRS2074816" ...
## ..$ BioSample : chr [1:20] "SAMN06645547" "SAMN06645546" "SAMN06645543" "SAMN06645542" ...
## ..$ SampleType : chr [1:20] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:20] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:20] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:20] NA NA NA NA NA NA ...
## ..$ source : logi [1:20] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:20] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:20] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:20] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:20] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:20] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:20] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:20] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:20] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:20] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:20] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:20] "SRA549619" "SRA549619" "SRA549619" "SRA549619" ...
## ..$ dbgap_study_accession: logi [1:20] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:20] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:20] "1A766C7E970969FBE27234C7F9B627F9" "64666A991C946DB1FF9504280BF07570" "EC10B8ED2652CCB65BF4950F0B943174" "E594A6E564A3B57BDDD8578E02B76795" ...
## ..$ ReadHash : chr [1:20] "898E731D7627CC3D75775BB9B89C3355" "22F018B04040C16C17B8D8697C58786A" "65B7030FADBD768FD346D362BCE406D1" "B9F7CC5224ED944F07E13730A1B7556E" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 15 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP102542: Genes expressed differentially in young people who do Resistance and HIIT training:Ctrl;SRX2676301,SRX2676307,SRX2676323,SRX2676335,SRX2676340,SRX2676344,SRX2676354,SRX2676366:R&H; SRX2676302,SRX2676308,SRX2676324,SRX2676341,SRX2676345,SRX2676355,SRX2676367## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 14 variables:
## ..$ SRR5381158: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381164: int [1:58302] 1 4 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381165: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381180: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381181: int [1:58302] 1 7 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381192: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381197: int [1:58302] 0 7 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381198: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381201: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381202: int [1:58302] 0 5 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381211: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381212: int [1:58302] 0 12 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381223: int [1:58302] 0 6 0 1 0 0 0 0 0 0 ...
## ..$ SRR5381224: int [1:58302] 0 9 1 1 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 14 variables:
## ..$ SRR5381158: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381164: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381165: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381180: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381181: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381192: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381197: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381198: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381201: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381202: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381211: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381212: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381223: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381224: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 14 variables:
## ..$ SRR5381158: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381164: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381165: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381180: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381181: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381192: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381197: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381198: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381201: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381202: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381211: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381212: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381223: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381224: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 14 obs. of 7 variables:
## ..$ QC_summary : chr [1:14] "WARN(8)" "WARN(8)" "PASS" "WARN(1,5,7,8)" ...
## ..$ SRX_accession: chr [1:14] "SRX2676301" "SRX2676307" "SRX2676308" "SRX2676323" ...
## ..$ SRS_accession: chr [1:14] "SRS2074808" "SRS2074812" "SRS2074813" "SRS2074827" ...
## ..$ SRP_accession: chr [1:14] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:14] "GSM2551324" "GSM2551330" "GSM2551331" "GSM2551346" ...
## ..$ GEO_series : chr [1:14] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:14] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 14 obs. of 52 variables:
## ..$ QC_summary : chr [1:14] "WARN(8)" "WARN(8)" "PASS" "WARN(1,5,7,8)" ...
## ..$ SRX_accession : chr [1:14] "SRX2676301" "SRX2676307" "SRX2676308" "SRX2676323" ...
## ..$ SRS_accession : chr [1:14] "SRS2074808" "SRS2074812" "SRS2074813" "SRS2074827" ...
## ..$ SRP_accession : chr [1:14] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:14] "GSM2551324" "GSM2551330" "GSM2551331" "GSM2551346" ...
## ..$ GEO_series : chr [1:14] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:14] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:14] "GSM2551324" "GSM2551330" "GSM2551331" "GSM2551346" ...
## ..$ ReleaseDate : chr [1:14] "2017-03-30 02:41:07" "2017-03-30 02:41:07" "2017-03-30 02:41:07" "2017-03-30 02:41:08" ...
## ..$ LoadDate : chr [1:14] "2017-03-27 16:35:07" "2017-03-27 16:40:21" "2017-03-27 16:38:12" "2017-03-27 16:35:56" ...
## ..$ spots : int [1:14] 14941036 26282970 26564722 9596122 20649593 31257765 19938399 9615123 29754651 27701566 ...
## ..$ bases : num [1:14] 1.52e+09 2.68e+09 2.71e+09 9.79e+08 2.11e+09 ...
## ..$ spots_with_mates : int [1:14] 14941036 26282970 26564722 9596122 20649593 31257765 19938399 9615123 29754651 27701566 ...
## ..$ avgLength : int [1:14] 102 102 102 102 102 102 102 102 102 102 ...
## ..$ size_MB : int [1:14] 943 1660 1653 588 1264 2088 1251 599 2040 1894 ...
## ..$ AssemblyName : logi [1:14] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:14] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381158/SRR5381158.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381164/SRR5381164.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381165/SRR5381165.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381180/SRR5381180.1" ...
## ..$ LibraryName : logi [1:14] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:14] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:14] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:14] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:14] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:14] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:14] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:14] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:14] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:14] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ BioProject : chr [1:14] "PRJNA380649" "PRJNA380649" "PRJNA380649" "PRJNA380649" ...
## ..$ Study_Pubmed_id : int [1:14] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:14] 380649 380649 380649 380649 380649 380649 380649 380649 380649 380649 ...
## ..$ Sample : chr [1:14] "SRS2074808" "SRS2074812" "SRS2074813" "SRS2074827" ...
## ..$ BioSample : chr [1:14] "SAMN06645551" "SAMN06645545" "SAMN06645544" "SAMN06645475" ...
## ..$ SampleType : chr [1:14] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:14] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:14] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:14] NA NA NA NA NA NA ...
## ..$ source : logi [1:14] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:14] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:14] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:14] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:14] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:14] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:14] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:14] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:14] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:14] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:14] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:14] "SRA549619" "SRA549619" "SRA549619" "SRA549619" ...
## ..$ dbgap_study_accession: logi [1:14] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:14] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:14] "F072D533E3C48445ACAA0318C43CF8F0" "DC9D42353DEFC979B689C715415BE29E" "0CDFF4DB5A6EAA89F67EB431328C473F" "A9AA111DABE071D1D150A87E2305DE87" ...
## ..$ ReadHash : chr [1:14] "FDDA8FDC4E9F40C68B848756C1526224" "0F60C523DF1B9008CEE7454747CD9A13" "AAEB8400AF15161B70456130F1E96832" "FEBD2A193738E639B6250C980DDE7290" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 18 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP102542: Genes expressed differentially in old people who do HIIT training:Ctrl; SRX2676325,SRX2676368,SRX2676374,SRX2676378,SRX2676384,SRX2676388,SRX2676390,SRX2676392:HIIT;SRX2676389,SRX2676391,SRX2676393,SRX2676326,SRX2676369,SRX2676375,SRX2676385,SRX2676379## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 16 variables:
## ..$ SRR5381182: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381183: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381225: int [1:58302] 0 9 2 0 0 0 0 0 0 0 ...
## ..$ SRR5381226: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR5381231: int [1:58302] 0 12 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381232: int [1:58302] 1 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381235: int [1:58302] 0 15 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381236: int [1:58302] 0 17 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381241: int [1:58302] 0 5 0 1 0 0 0 0 0 0 ...
## ..$ SRR5381242: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381245: int [1:58302] 0 8 0 1 0 0 0 0 0 0 ...
## ..$ SRR5381246: int [1:58302] 0 7 1 1 0 0 0 0 0 0 ...
## ..$ SRR5381247: int [1:58302] 0 19 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381248: int [1:58302] 0 10 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381249: int [1:58302] 0 8 0 1 0 0 0 0 0 0 ...
## ..$ SRR5381250: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 16 variables:
## ..$ SRR5381182: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381183: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381225: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381226: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381231: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381232: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381235: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381236: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381241: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381242: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381245: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381246: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381247: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381248: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381249: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381250: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 16 variables:
## ..$ SRR5381182: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381183: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381225: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381226: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381231: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381232: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381235: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381236: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381241: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381242: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381245: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381246: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381247: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381248: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381249: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381250: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 16 obs. of 7 variables:
## ..$ QC_summary : chr [1:16] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:16] "SRX2676325" "SRX2676326" "SRX2676368" "SRX2676369" ...
## ..$ SRS_accession: chr [1:16] "SRS2074830" "SRS2074831" "SRS2074873" "SRS2074874" ...
## ..$ SRP_accession: chr [1:16] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:16] "GSM2551348" "GSM2551349" "GSM2551391" "GSM2551392" ...
## ..$ GEO_series : chr [1:16] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 16 obs. of 52 variables:
## ..$ QC_summary : chr [1:16] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:16] "SRX2676325" "SRX2676326" "SRX2676368" "SRX2676369" ...
## ..$ SRS_accession : chr [1:16] "SRS2074830" "SRS2074831" "SRS2074873" "SRS2074874" ...
## ..$ SRP_accession : chr [1:16] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:16] "GSM2551348" "GSM2551349" "GSM2551391" "GSM2551392" ...
## ..$ GEO_series : chr [1:16] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:16] "GSM2551348" "GSM2551349" "GSM2551391" "GSM2551392" ...
## ..$ ReleaseDate : chr [1:16] "2017-03-30 02:41:08" "2017-03-30 02:41:08" "2017-03-30 02:41:09" "2017-03-30 02:41:09" ...
## ..$ LoadDate : chr [1:16] "2017-03-27 16:36:43" "2017-03-27 16:38:20" "2017-03-27 16:42:23" "2017-03-27 16:41:22" ...
## ..$ spots : int [1:16] 14712334 17656796 28028069 20023943 29727584 17268122 31220859 25866398 23820496 23269252 ...
## ..$ bases : num [1:16] 1.50e+09 1.80e+09 2.86e+09 2.04e+09 3.03e+09 ...
## ..$ spots_with_mates : int [1:16] 14712334 17656796 28028069 20023943 29727584 17268122 31220859 25866398 23820496 23269252 ...
## ..$ avgLength : int [1:16] 102 102 102 102 102 102 102 102 102 102 ...
## ..$ size_MB : int [1:16] 904 1089 1813 1284 1892 1094 2151 1776 1499 1461 ...
## ..$ AssemblyName : logi [1:16] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:16] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381182/SRR5381182.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381183/SRR5381183.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381225/SRR5381225.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381226/SRR5381226.1" ...
## ..$ LibraryName : logi [1:16] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:16] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:16] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:16] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:16] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:16] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:16] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:16] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ BioProject : chr [1:16] "PRJNA380649" "PRJNA380649" "PRJNA380649" "PRJNA380649" ...
## ..$ Study_Pubmed_id : int [1:16] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:16] 380649 380649 380649 380649 380649 380649 380649 380649 380649 380649 ...
## ..$ Sample : chr [1:16] "SRS2074830" "SRS2074831" "SRS2074873" "SRS2074874" ...
## ..$ BioSample : chr [1:16] "SAMN06645532" "SAMN06645467" "SAMN06645492" "SAMN06645491" ...
## ..$ SampleType : chr [1:16] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:16] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:16] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:16] NA NA NA NA NA NA ...
## ..$ source : logi [1:16] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:16] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:16] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:16] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:16] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:16] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:16] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:16] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:16] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:16] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:16] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:16] "SRA549619" "SRA549619" "SRA549619" "SRA549619" ...
## ..$ dbgap_study_accession: logi [1:16] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:16] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:16] "4153B9FBCC858EE35CC803C2EBBE1D24" "0346F1675E4B5386607FB3CFB7B4B625" "F3FF819C232D2D16CB324C4EED76B3B7" "375D571EE17BAF9E12E020C72CAF27B2" ...
## ..$ ReadHash : chr [1:16] "2AEA9FE59914D97C6D312594227B607E" "3413248483D7D30A5BDA7A0968B16664" "06010AA9C95AFDD3CDB11CB052CE4CEE" "FA7348A800ACB1032EFB50C69F6CC3DF" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 39 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP102542: Genes expressed differentially in old people who do resistance training:Ctrl; SRX2676336,SRX2676350,SRX2676370,SRX2676372,SRX2676382,SRX2676386,SRX2676400,SRX2676402:Resis; SRX2676337,SRX2676351,SRX2676371,SRX2676373,SRX2676383,SRX2676387,SRX2676401,SRX2676403## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 16 variables:
## ..$ SRR5381193: int [1:58302] 1 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381194: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381207: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381208: int [1:58302] 1 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381227: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381228: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381229: int [1:58302] 0 18 3 1 0 0 0 0 0 0 ...
## ..$ SRR5381230: int [1:58302] 0 6 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381239: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381240: int [1:58302] 0 5 0 1 0 0 0 0 0 0 ...
## ..$ SRR5381243: int [1:58302] 0 13 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381244: int [1:58302] 0 6 1 1 0 0 0 0 0 0 ...
## ..$ SRR5381257: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381258: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381259: int [1:58302] 0 9 0 1 0 0 0 0 0 0 ...
## ..$ SRR5381260: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 16 variables:
## ..$ SRR5381193: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381194: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381207: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381208: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381227: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381228: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381229: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381230: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381239: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381240: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381243: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381244: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381257: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381258: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381259: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381260: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 16 variables:
## ..$ SRR5381193: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381194: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381207: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381208: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381227: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381228: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381229: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381230: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381239: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381240: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381243: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381244: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381257: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381258: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381259: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381260: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 16 obs. of 7 variables:
## ..$ QC_summary : chr [1:16] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:16] "SRX2676336" "SRX2676337" "SRX2676350" "SRX2676351" ...
## ..$ SRS_accession: chr [1:16] "SRS2074840" "SRS2074841" "SRS2074855" "SRS2074856" ...
## ..$ SRP_accession: chr [1:16] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:16] "GSM2551359" "GSM2551360" "GSM2551373" "GSM2551374" ...
## ..$ GEO_series : chr [1:16] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 16 obs. of 52 variables:
## ..$ QC_summary : chr [1:16] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:16] "SRX2676336" "SRX2676337" "SRX2676350" "SRX2676351" ...
## ..$ SRS_accession : chr [1:16] "SRS2074840" "SRS2074841" "SRS2074855" "SRS2074856" ...
## ..$ SRP_accession : chr [1:16] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:16] "GSM2551359" "GSM2551360" "GSM2551373" "GSM2551374" ...
## ..$ GEO_series : chr [1:16] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:16] "GSM2551359" "GSM2551360" "GSM2551373" "GSM2551374" ...
## ..$ ReleaseDate : chr [1:16] "2017-03-30 02:41:08" "2017-03-30 02:41:08" "2017-03-30 02:41:08" "2017-03-30 02:41:08" ...
## ..$ LoadDate : chr [1:16] "2017-03-27 16:40:12" "2017-03-27 16:40:55" "2017-03-27 16:42:26" "2017-03-27 16:39:45" ...
## ..$ spots : int [1:16] 24855453 28571113 27169296 21248671 17886086 24890907 39524527 27778032 28147516 26011707 ...
## ..$ bases : num [1:16] 2.54e+09 2.91e+09 2.77e+09 2.17e+09 1.82e+09 ...
## ..$ spots_with_mates : int [1:16] 24855453 28571113 27169296 21248671 17886086 24890907 39524527 27778032 28147516 26011707 ...
## ..$ avgLength : int [1:16] 102 102 102 102 102 102 102 102 102 102 ...
## ..$ size_MB : int [1:16] 1659 1898 1760 1379 1160 1610 2705 1906 1931 1787 ...
## ..$ AssemblyName : logi [1:16] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:16] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381193/SRR5381193.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381194/SRR5381194.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381207/SRR5381207.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381208/SRR5381208.1" ...
## ..$ LibraryName : logi [1:16] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:16] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:16] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:16] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:16] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:16] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:16] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:16] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ BioProject : chr [1:16] "PRJNA380649" "PRJNA380649" "PRJNA380649" "PRJNA380649" ...
## ..$ Study_Pubmed_id : int [1:16] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:16] 380649 380649 380649 380649 380649 380649 380649 380649 380649 380649 ...
## ..$ Sample : chr [1:16] "SRS2074840" "SRS2074841" "SRS2074855" "SRS2074856" ...
## ..$ BioSample : chr [1:16] "SAMN06645464" "SAMN06645463" "SAMN06645450" "SAMN06645449" ...
## ..$ SampleType : chr [1:16] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:16] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:16] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:16] NA NA NA NA NA NA ...
## ..$ source : logi [1:16] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:16] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:16] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:16] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:16] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:16] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:16] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:16] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:16] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:16] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:16] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:16] "SRA549619" "SRA549619" "SRA549619" "SRA549619" ...
## ..$ dbgap_study_accession: logi [1:16] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:16] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:16] "F1A7140D124C4062A7A9B48348F8509D" "515CE2FC27654256F71AD3F030E832F5" "4AE00DE691CCD812DE4FA67F96C17D05" "0653AA0241591EEA5604483A2ED80B65" ...
## ..$ ReadHash : chr [1:16] "54E68F0CC71CB770D1B6B442E94F5E7A" "AFA314C2CD1CED754EA21212ED6F9DF6" "B4C639BED7FAF03AA0FFC22B0F4CCC5B" "6A51CFACCB674F47E3D233A06748BFD6" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 75 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP102542: Genes expressed differentially in old people who do Resistance and HIIT training:Ctrl;SRX2676319,SRX2676321,SRX2676356,SRX2676376,SRX2676380,SRX2676394,SRX2676398:H&R; SRX2676320,SRX2676322,SRX2676341,SRX2676377,SRX2676381,SRX2676395,SRX2676399## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 14 variables:
## ..$ SRR5381176: int [1:58302] 0 4 0 1 0 0 0 0 0 0 ...
## ..$ SRR5381177: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381178: int [1:58302] 1 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381179: int [1:58302] 0 2 2 0 0 0 0 0 0 0 ...
## ..$ SRR5381198: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381213: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381233: int [1:58302] 0 9 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381234: int [1:58302] 0 5 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381237: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381238: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR5381251: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381252: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381255: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381256: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 14 variables:
## ..$ SRR5381176: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381177: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381178: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381179: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381198: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381213: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381233: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381234: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381237: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381238: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381251: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381252: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381255: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5381256: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 14 variables:
## ..$ SRR5381176: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381177: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381178: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381179: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381198: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381213: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381233: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381234: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381237: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381238: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381251: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381252: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381255: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5381256: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 14 obs. of 7 variables:
## ..$ QC_summary : chr [1:14] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(1,5,7,8)" ...
## ..$ SRX_accession: chr [1:14] "SRX2676319" "SRX2676320" "SRX2676321" "SRX2676322" ...
## ..$ SRS_accession: chr [1:14] "SRS2074824" "SRS2074826" "SRS2074825" "SRS2074829" ...
## ..$ SRP_accession: chr [1:14] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:14] "GSM2551342" "GSM2551343" "GSM2551344" "GSM2551345" ...
## ..$ GEO_series : chr [1:14] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:14] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 14 obs. of 52 variables:
## ..$ QC_summary : chr [1:14] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(1,5,7,8)" ...
## ..$ SRX_accession : chr [1:14] "SRX2676319" "SRX2676320" "SRX2676321" "SRX2676322" ...
## ..$ SRS_accession : chr [1:14] "SRS2074824" "SRS2074826" "SRS2074825" "SRS2074829" ...
## ..$ SRP_accession : chr [1:14] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ Sample_name : chr [1:14] "GSM2551342" "GSM2551343" "GSM2551344" "GSM2551345" ...
## ..$ GEO_series : chr [1:14] "GSE97084" "GSE97084" "GSE97084" "GSE97084" ...
## ..$ Library_name : logi [1:14] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:14] "GSM2551342" "GSM2551343" "GSM2551344" "GSM2551345" ...
## ..$ ReleaseDate : chr [1:14] "2017-03-30 02:41:07" "2017-03-30 02:41:07" "2017-03-30 02:41:08" "2017-03-30 02:41:08" ...
## ..$ LoadDate : chr [1:14] "2017-03-27 16:38:25" "2017-03-27 16:36:22" "2017-03-27 16:37:30" "2017-03-27 16:35:52" ...
## ..$ spots : int [1:14] 26361062 22001876 24051560 7879266 9615123 19202638 32653647 32010862 25032826 31561836 ...
## ..$ bases : num [1:14] 2.69e+09 2.24e+09 2.45e+09 8.04e+08 9.81e+08 ...
## ..$ spots_with_mates : int [1:14] 26361062 22001876 24051560 7879266 9615123 19202638 32653647 32010862 25032826 31561836 ...
## ..$ avgLength : int [1:14] 102 102 102 102 102 102 102 102 102 102 ...
## ..$ size_MB : int [1:14] 1658 1383 1478 482 599 1243 2253 2196 1721 2159 ...
## ..$ AssemblyName : logi [1:14] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:14] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381176/SRR5381176.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381177/SRR5381177.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381178/SRR5381178.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5381179/SRR5381179.1" ...
## ..$ LibraryName : logi [1:14] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:14] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:14] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:14] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:14] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:14] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:14] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:14] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:14] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:14] "SRP102542" "SRP102542" "SRP102542" "SRP102542" ...
## ..$ BioProject : chr [1:14] "PRJNA380649" "PRJNA380649" "PRJNA380649" "PRJNA380649" ...
## ..$ Study_Pubmed_id : int [1:14] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:14] 380649 380649 380649 380649 380649 380649 380649 380649 380649 380649 ...
## ..$ Sample : chr [1:14] "SRS2074824" "SRS2074826" "SRS2074825" "SRS2074829" ...
## ..$ BioSample : chr [1:14] "SAMN06645531" "SAMN06645478" "SAMN06645477" "SAMN06645476" ...
## ..$ SampleType : chr [1:14] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:14] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:14] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:14] NA NA NA NA NA NA ...
## ..$ source : logi [1:14] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:14] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:14] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:14] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:14] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:14] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:14] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:14] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:14] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:14] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:14] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:14] "SRA549619" "SRA549619" "SRA549619" "SRA549619" ...
## ..$ dbgap_study_accession: logi [1:14] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:14] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:14] "2EB800574D3A0531168F897932C0A5CD" "067E3D527D8DAA41B14F21981A35344F" "69CE2CC9AC2CBD6DD75A71D5493A2761" "520BC777C748E661272D821F42C48874" ...
## ..$ ReadHash : chr [1:14] "9AD4BE0C386891281F931DD356A5C6EE" "420F3BDA6BC662D76A9E38C157EE7E8E" "2193FB52C23425E6CE77D6FB66B9B3DC" "3383938D2DEF86AA2E39E055116013E7" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 6 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP097696: retinal endothelial cells from non-diabetic controls versus fibrovascular membrane endothelial cells from proliferative diabetic retinopathy: non-diabetic control; SRX2513447, SRX2513448, SRX2513458, SRX2513459: proliferative diabetic retinopathy; SRX2513449, SRX2513450, SRX2513451, SRX2513452, SRX2513453, SRX2513454, SRX2513455, SRX2513456, SRX2513457;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 13 variables:
## ..$ SRR5197972: int [1:58302] 5 0 0 1 0 0 0 0 0 2 ...
## ..$ SRR5197973: int [1:58302] 2 0 0 1 0 0 0 9 5 1 ...
## ..$ SRR5197974: int [1:58302] 0 6 0 0 0 0 0 5 0 3 ...
## ..$ SRR5197975: int [1:58302] 1 7 0 0 0 0 0 0 0 1 ...
## ..$ SRR5197976: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197977: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197978: int [1:58302] 0 0 0 0 0 0 0 0 0 3 ...
## ..$ SRR5197979: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197980: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197981: int [1:58302] 0 7 0 0 0 0 19 0 0 0 ...
## ..$ SRR5197982: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197983: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197984: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 13 variables:
## ..$ SRR5197972: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197973: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197974: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197975: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197976: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197977: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197978: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197982: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197983: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5197984: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 13 variables:
## ..$ SRR5197972: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197973: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197974: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197975: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197976: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197977: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197978: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197979: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197980: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197981: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197982: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197983: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR5197984: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## $ MetadataSummary:'data.frame': 13 obs. of 7 variables:
## ..$ QC_summary : chr [1:13] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession: chr [1:13] "SRX2513447" "SRX2513448" "SRX2513449" "SRX2513450" ...
## ..$ SRS_accession: chr [1:13] "SRS1936981" "SRS1936982" "SRS1936983" "SRS1936984" ...
## ..$ SRP_accession: chr [1:13] "SRP097696" "SRP097696" "SRP097696" "SRP097696" ...
## ..$ Sample_name : chr [1:13] "GSM2467179" "GSM2467180" "GSM2467181" "GSM2467182" ...
## ..$ GEO_series : chr [1:13] "GSE94019" "GSE94019" "GSE94019" "GSE94019" ...
## ..$ Library_name : logi [1:13] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 13 obs. of 52 variables:
## ..$ QC_summary : chr [1:13] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" ...
## ..$ SRX_accession : chr [1:13] "SRX2513447" "SRX2513448" "SRX2513449" "SRX2513450" ...
## ..$ SRS_accession : chr [1:13] "SRS1936981" "SRS1936982" "SRS1936983" "SRS1936984" ...
## ..$ SRP_accession : chr [1:13] "SRP097696" "SRP097696" "SRP097696" "SRP097696" ...
## ..$ Sample_name : chr [1:13] "GSM2467179" "GSM2467180" "GSM2467181" "GSM2467182" ...
## ..$ GEO_series : chr [1:13] "GSE94019" "GSE94019" "GSE94019" "GSE94019" ...
## ..$ Library_name : logi [1:13] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:13] "GSM2467179" "GSM2467180" "GSM2467181" "GSM2467182" ...
## ..$ ReleaseDate : chr [1:13] "2017-04-05 08:17:19" "2017-04-05 08:17:19" "2017-04-05 08:17:19" "2017-04-05 08:17:19" ...
## ..$ LoadDate : chr [1:13] "2017-01-24 16:01:38" "2017-01-24 16:06:33" "2017-01-24 16:07:09" "2017-01-24 16:05:32" ...
## ..$ spots : int [1:13] 19620727 23917805 25547211 26292451 15682212 9935282 18914335 37657822 22101719 28306560 ...
## ..$ bases : num [1:13] 2.94e+09 3.59e+09 3.83e+09 3.94e+09 2.35e+09 ...
## ..$ spots_with_mates : int [1:13] 19620727 23917805 25547211 26292451 15682212 9935282 18914335 37657822 22101719 28306560 ...
## ..$ avgLength : int [1:13] 150 150 150 150 150 150 150 150 150 150 ...
## ..$ size_MB : int [1:13] 1717 2072 2248 2359 1401 878 1584 3178 1845 2387 ...
## ..$ AssemblyName : logi [1:13] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:13] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR5197972/SRR5197972.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5197973/SRR5197973.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5197974/SRR5197974.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR5197975/SRR5197975.1" ...
## ..$ LibraryName : logi [1:13] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:13] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:13] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:13] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:13] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:13] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:13] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:13] "SRP097696" "SRP097696" "SRP097696" "SRP097696" ...
## ..$ BioProject : chr [1:13] "PRJNA363068" "PRJNA363068" "PRJNA363068" "PRJNA363068" ...
## ..$ Study_Pubmed_id : int [1:13] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:13] 363068 363068 363068 363068 363068 363068 363068 363068 363068 363068 ...
## ..$ Sample : chr [1:13] "SRS1936981" "SRS1936982" "SRS1936983" "SRS1936984" ...
## ..$ BioSample : chr [1:13] "SAMN06252883" "SAMN06252882" "SAMN06252881" "SAMN06252880" ...
## ..$ SampleType : chr [1:13] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:13] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:13] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:13] NA NA NA NA NA NA ...
## ..$ source : logi [1:13] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:13] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:13] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:13] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:13] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:13] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:13] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:13] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:13] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:13] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:13] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:13] "SRA531096" "SRA531096" "SRA531096" "SRA531096" ...
## ..$ dbgap_study_accession: logi [1:13] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:13] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:13] "B446AD554FA2322A88A19427831E0EC6" "AE95D11698414C4D45C6CE55FD3DC242" "ACB317F3EEC6808D62FA12B5B3A4C8F3" "6B8B4EFF2C303E70E14AF4FDB3100EDF" ...
## ..$ ReadHash : chr [1:13] "7ED82F632846B3B5F3F5D7D5F3FADBEC" "070ECF53B439BAC65399F104CDFB74E6" "6CA119A4857DC9086A5B047073B74BC1" "3091DF5CA59538ADBC8DA5311E52E75E" ...
## $ absent : chr(0)## SRP101810: bulk-cell RNA-seq of unstimulated T cell clone versus anti-CD3 anti-CD28 monoclonal antibodies stimulated T cell clone: unstimulated T cell clone; SRX2637128, SRX2637129, SRX2637130: anti-CD3 anti-CD28 stimulated T cell clone; SRX2637126, SRX2637131, SRX2637133;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR5340384: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340386: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340387: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340388: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340389: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340391: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR5340384: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340386: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340387: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340388: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340389: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340391: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR5340384: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340386: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340387: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340388: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340389: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340391: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(3,4,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:6] "SRX2637126" "SRX2637128" "SRX2637129" "SRX2637130" ...
## ..$ SRS_accession: chr [1:6] "SRS2045219" "SRS2045221" "SRS2045222" "SRS2045223" ...
## ..$ SRP_accession: chr [1:6] "SRP101810" "SRP101810" "SRP101810" "SRP101810" ...
## ..$ Sample_name : chr [1:6] "GSM2535785" "GSM2535787" "GSM2535788" "GSM2535789" ...
## ..$ GEO_series : chr [1:6] "GSE96563" "GSE96563" "GSE96563" "GSE96563" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(3,4,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:6] "SRX2637126" "SRX2637128" "SRX2637129" "SRX2637130" ...
## ..$ SRS_accession : chr [1:6] "SRS2045219" "SRS2045221" "SRS2045222" "SRS2045223" ...
## ..$ SRP_accession : chr [1:6] "SRP101810" "SRP101810" "SRP101810" "SRP101810" ...
## ..$ Sample_name : chr [1:6] "GSM2535785" "GSM2535787" "GSM2535788" "GSM2535789" ...
## ..$ GEO_series : chr [1:6] "GSE96563" "GSE96563" "GSE96563" "GSE96563" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2535785" "GSM2535787" "GSM2535788" "GSM2535789" ...
## ..$ ReleaseDate : chr [1:6] "2017-06-08 15:46:56" "2017-06-08 15:46:56" "2017-06-08 15:46:56" "2017-06-08 15:46:56" ...
## ..$ LoadDate : chr [1:6] "2017-03-14 11:39:56" "2017-03-14 11:36:57" "2017-03-14 11:38:11" "2017-03-14 11:37:05" ...
## ..$ spots : int [1:6] 10998947 6829335 5211906 6380184 7421217 7017079
## ..$ bases : int [1:6] 1099894700 682933500 521190600 638018400 742121700 701707900
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 100 100 100 100 100 100
## ..$ size_MB : int [1:6] 691 432 333 405 465 439
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340384/SRR5340384.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340386/SRR5340386.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340387/SRR5340387.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340388/SRR5340388.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:6] "SRP101810" "SRP101810" "SRP101810" "SRP101810" ...
## ..$ BioProject : chr [1:6] "PRJNA379012" "PRJNA379012" "PRJNA379012" "PRJNA379012" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 379012 379012 379012 379012 379012 379012
## ..$ Sample : chr [1:6] "SRS2045219" "SRS2045221" "SRS2045222" "SRS2045223" ...
## ..$ BioSample : chr [1:6] "SAMN06565407" "SAMN06565405" "SAMN06565404" "SAMN06565403" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA545472" "SRA545472" "SRA545472" "SRA545472" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "0683E19DB0A1B4BA144F116CF5B7B16C" "6FBD95A1F2F73846612D447262CA6F2E" "794D145BD86E3198C5FC6A3FEE1F2420" "111A6AA704C84F18F98111CD88D5E407" ...
## ..$ ReadHash : chr [1:6] "83E5774923F531782746EF2A47CDADB1" "6F5CDD868D83C286BF67566ED9CC85E1" "602D631A236D22FFC2798E413C5B36CF" "8A505B3BAE202A913C9FA7C4EAF05EF6" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP101810: bulk-cell RNA-seq of unstimulated T cell clone versus GAD peptide-loaded tetramer stimulated T cell clone: unstimulated T cell clone; SRX2637128, SRX2637129, SRX2637130: tetramer stimulated T cell clone; SRX2637127, SRX2637132, SRX2637134;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR5340385: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340386: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340387: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340388: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340390: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340392: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR5340385: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340386: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340387: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340388: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340390: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340392: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR5340385: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340386: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340387: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340388: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340390: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340392: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(1,3,4,5,6,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:6] "SRX2637127" "SRX2637128" "SRX2637129" "SRX2637130" ...
## ..$ SRS_accession: chr [1:6] "SRS2045220" "SRS2045221" "SRS2045222" "SRS2045223" ...
## ..$ SRP_accession: chr [1:6] "SRP101810" "SRP101810" "SRP101810" "SRP101810" ...
## ..$ Sample_name : chr [1:6] "GSM2535786" "GSM2535787" "GSM2535788" "GSM2535789" ...
## ..$ GEO_series : chr [1:6] "GSE96563" "GSE96563" "GSE96563" "GSE96563" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(1,3,4,5,6,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:6] "SRX2637127" "SRX2637128" "SRX2637129" "SRX2637130" ...
## ..$ SRS_accession : chr [1:6] "SRS2045220" "SRS2045221" "SRS2045222" "SRS2045223" ...
## ..$ SRP_accession : chr [1:6] "SRP101810" "SRP101810" "SRP101810" "SRP101810" ...
## ..$ Sample_name : chr [1:6] "GSM2535786" "GSM2535787" "GSM2535788" "GSM2535789" ...
## ..$ GEO_series : chr [1:6] "GSE96563" "GSE96563" "GSE96563" "GSE96563" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2535786" "GSM2535787" "GSM2535788" "GSM2535789" ...
## ..$ ReleaseDate : chr [1:6] "2017-06-08 15:46:56" "2017-06-08 15:46:56" "2017-06-08 15:46:56" "2017-06-08 15:46:56" ...
## ..$ LoadDate : chr [1:6] "2017-03-14 11:37:53" "2017-03-14 11:36:57" "2017-03-14 11:38:11" "2017-03-14 11:37:05" ...
## ..$ spots : int [1:6] 8131630 6829335 5211906 6380184 8777656 8108820
## ..$ bases : int [1:6] 813163000 682933500 521190600 638018400 877765600 810882000
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 100 100 100 100 100 100
## ..$ size_MB : int [1:6] 509 432 333 405 554 508
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340385/SRR5340385.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340386/SRR5340386.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340387/SRR5340387.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340388/SRR5340388.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:6] "SRP101810" "SRP101810" "SRP101810" "SRP101810" ...
## ..$ BioProject : chr [1:6] "PRJNA379012" "PRJNA379012" "PRJNA379012" "PRJNA379012" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 379012 379012 379012 379012 379012 379012
## ..$ Sample : chr [1:6] "SRS2045220" "SRS2045221" "SRS2045222" "SRS2045223" ...
## ..$ BioSample : chr [1:6] "SAMN06565406" "SAMN06565405" "SAMN06565404" "SAMN06565403" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA545472" "SRA545472" "SRA545472" "SRA545472" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "4FBE539E40B8A551E1C3D6489280475D" "6FBD95A1F2F73846612D447262CA6F2E" "794D145BD86E3198C5FC6A3FEE1F2420" "111A6AA704C84F18F98111CD88D5E407" ...
## ..$ ReadHash : chr [1:6] "2EA0936D61928DDDB490E323033D2E0C" "6F5CDD868D83C286BF67566ED9CC85E1" "602D631A236D22FFC2798E413C5B36CF" "8A505B3BAE202A913C9FA7C4EAF05EF6" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## SRP101810: bulk-cell RNA-seq of anti-CD3 anti-CD28 monoclonal antibodies stimulated T cell clone versus GAD peptide-loaded tetramer stimulated T cell clone: anti-CD3 anti-CD28 stimulated T cell clone; SRX2637126, SRX2637131, SRX2637133: tetramer stimulated T cell clone; SRX2637127, SRX2637132, SRX2637134;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 6 variables:
## ..$ SRR5340384: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340385: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340389: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340390: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340391: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340392: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR5340384: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340385: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340389: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340390: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340391: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5340392: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR5340384: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340385: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340389: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340390: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340391: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5340392: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(3,4,5,7)" "WARN(1,3,4,5,6,7)" "WARN(1,3,4,5,7)" "WARN(1,3,4,5,6,7)" ...
## ..$ SRX_accession: chr [1:6] "SRX2637126" "SRX2637127" "SRX2637131" "SRX2637132" ...
## ..$ SRS_accession: chr [1:6] "SRS2045219" "SRS2045220" "SRS2045224" "SRS2045225" ...
## ..$ SRP_accession: chr [1:6] "SRP101810" "SRP101810" "SRP101810" "SRP101810" ...
## ..$ Sample_name : chr [1:6] "GSM2535785" "GSM2535786" "GSM2535790" "GSM2535791" ...
## ..$ GEO_series : chr [1:6] "GSE96563" "GSE96563" "GSE96563" "GSE96563" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(3,4,5,7)" "WARN(1,3,4,5,6,7)" "WARN(1,3,4,5,7)" "WARN(1,3,4,5,6,7)" ...
## ..$ SRX_accession : chr [1:6] "SRX2637126" "SRX2637127" "SRX2637131" "SRX2637132" ...
## ..$ SRS_accession : chr [1:6] "SRS2045219" "SRS2045220" "SRS2045224" "SRS2045225" ...
## ..$ SRP_accession : chr [1:6] "SRP101810" "SRP101810" "SRP101810" "SRP101810" ...
## ..$ Sample_name : chr [1:6] "GSM2535785" "GSM2535786" "GSM2535790" "GSM2535791" ...
## ..$ GEO_series : chr [1:6] "GSE96563" "GSE96563" "GSE96563" "GSE96563" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2535785" "GSM2535786" "GSM2535790" "GSM2535791" ...
## ..$ ReleaseDate : chr [1:6] "2017-06-08 15:46:56" "2017-06-08 15:46:56" "2017-06-08 15:46:56" "2017-06-08 15:46:56" ...
## ..$ LoadDate : chr [1:6] "2017-03-14 11:39:56" "2017-03-14 11:37:53" "2017-03-14 11:39:44" "2017-03-14 11:38:28" ...
## ..$ spots : int [1:6] 10998947 8131630 7421217 8777656 7017079 8108820
## ..$ bases : int [1:6] 1099894700 813163000 742121700 877765600 701707900 810882000
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 100 100 100 100 100 100
## ..$ size_MB : int [1:6] 691 509 465 554 439 508
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340384/SRR5340384.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340385/SRR5340385.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340389/SRR5340389.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5340390/SRR5340390.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" "Illumina HiScanSQ" ...
## ..$ SRAStudy : chr [1:6] "SRP101810" "SRP101810" "SRP101810" "SRP101810" ...
## ..$ BioProject : chr [1:6] "PRJNA379012" "PRJNA379012" "PRJNA379012" "PRJNA379012" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 379012 379012 379012 379012 379012 379012
## ..$ Sample : chr [1:6] "SRS2045219" "SRS2045220" "SRS2045224" "SRS2045225" ...
## ..$ BioSample : chr [1:6] "SAMN06565407" "SAMN06565406" "SAMN06565402" "SAMN06565401" ...
## ..$ SampleType : chr [1:6] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:6] 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:6] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:6] NA NA NA NA NA NA
## ..$ source : logi [1:6] NA NA NA NA NA NA
## ..$ g1k_analysis_group : logi [1:6] NA NA NA NA NA NA
## ..$ Subject_ID : logi [1:6] NA NA NA NA NA NA
## ..$ Sex : logi [1:6] NA NA NA NA NA NA
## ..$ Disease : logi [1:6] NA NA NA NA NA NA
## ..$ Tumor : chr [1:6] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:6] NA NA NA NA NA NA
## ..$ Analyte_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Histological_Type : logi [1:6] NA NA NA NA NA NA
## ..$ Body_Site : logi [1:6] NA NA NA NA NA NA
## ..$ CenterName : chr [1:6] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:6] "SRA545472" "SRA545472" "SRA545472" "SRA545472" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "0683E19DB0A1B4BA144F116CF5B7B16C" "4FBE539E40B8A551E1C3D6489280475D" "A31BF636E9C212A444CD28F97F21AAB2" "E74B51A929677D1BCA379FB472B7C9BD" ...
## ..$ ReadHash : chr [1:6] "83E5774923F531782746EF2A47CDADB1" "2EA0936D61928DDDB490E323033D2E0C" "2914C3104BC5671271BB63F8FF2EEECD" "2A993798F3B2264E57845FE19C06DDE5" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
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## [1] 8data <- data[which(lapply(data,length)>1)]
data <- data[which(lapply(data,function(x) length(x[[5]] ))>0)]
saveRDS(data,"diabetes_data.rds")
gs1 <- lapply(data, function(x) { x[5] })
gs2 <- lapply(data, function(x) { x[6] })
gs <- c(gs1,gs2)
gs <- lapply(gs,function(x) x[[1]] )
gs <- gs[which(lapply(gs,length)==3)]
attributes(gs)$class <- "GMT"
write.GMT(gs,"diabetes_ensemblIDs.gmt")
gs1 <- lapply(data, function(x) { x[7] })
gs2 <- lapply(data, function(x) { x[8] })
gs <- c(gs1,gs2)
gs <- lapply(gs,function(x) x[[1]] )
gs <- lapply(gs,function(x) { x[[3]] <- unique(x[[3]] ) ; return(x) } )
gs <- gs[which(lapply(gs,length)==3)]
attributes(gs)$class <- "GMT"
write.GMT(gs,"diabetes_genesymbols.gmt")sessionInfo()## R version 4.0.2 (2020-06-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] edgeR_3.30.3 limma_3.44.3
## [3] DESeq2_1.28.1 SummarizedExperiment_1.18.2
## [5] DelayedArray_0.14.1 matrixStats_0.57.0
## [7] Biobase_2.48.0 GenomicRanges_1.40.0
## [9] GenomeInfoDb_1.24.2 IRanges_2.22.2
## [11] S4Vectors_0.26.1 BiocGenerics_0.34.0
## [13] getDEE2_0.99.30 gplots_3.1.0
## [15] ActivePathways_1.0.2 devtools_2.3.2
## [17] usethis_1.6.3
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 fs_1.5.0 bit64_4.0.5
## [4] RColorBrewer_1.1-2 rprojroot_1.3-2 tools_4.0.2
## [7] backports_1.1.10 R6_2.4.1 KernSmooth_2.23-17
## [10] DBI_1.1.0 colorspace_1.4-1 htm2txt_2.1.1
## [13] withr_2.3.0 tidyselect_1.1.0 prettyunits_1.1.1
## [16] processx_3.4.4 bit_4.0.4 compiler_4.0.2
## [19] cli_2.0.2 desc_1.2.0 caTools_1.18.0
## [22] scales_1.1.1 genefilter_1.70.0 callr_3.5.0
## [25] stringr_1.4.0 digest_0.6.25 rmarkdown_2.4
## [28] XVector_0.28.0 pkgconfig_2.0.3 htmltools_0.5.0
## [31] sessioninfo_1.1.1 rlang_0.4.8 RSQLite_2.2.1
## [34] generics_0.0.2 BiocParallel_1.22.0 gtools_3.8.2
## [37] dplyr_1.0.2 RCurl_1.98-1.2 magrittr_1.5
## [40] GenomeInfoDbData_1.2.3 Matrix_1.2-18 Rcpp_1.0.5
## [43] munsell_0.5.0 fansi_0.4.1 lifecycle_0.2.0
## [46] stringi_1.5.3 yaml_2.2.1 zlibbioc_1.34.0
## [49] pkgbuild_1.1.0 grid_4.0.2 blob_1.2.1
## [52] crayon_1.3.4 lattice_0.20-41 splines_4.0.2
## [55] annotate_1.66.0 locfit_1.5-9.4 knitr_1.30
## [58] ps_1.4.0 pillar_1.4.6 geneplotter_1.66.0
## [61] pkgload_1.1.0 XML_3.99-0.5 glue_1.4.2
## [64] evaluate_0.14 data.table_1.13.0 remotes_2.2.0
## [67] vctrs_0.3.4 testthat_2.3.2 gtable_0.3.0
## [70] purrr_0.3.4 assertthat_0.2.1 ggplot2_3.3.2
## [73] xfun_0.18 xtable_1.8-4 survival_3.2-7
## [76] tibble_3.0.3 AnnotationDbi_1.50.3 memoise_1.1.0
## [79] ellipsis_0.3.1