MERS, SARS and SARS-CoV-2
The Gene Signature Commons Group
2020-10-17
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/SARS_MERS.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] 63# get the metadata now to save time
mdat <- getDEE2::getDEE2Metadata(species = SPECIES)
# lets prototype this: main(x[[2]])
# debug like this: x1 <- x[[15]]
# now go ahead and run the whole thing
data <- lapply(x,function(x) { main(x,mdat) })## SRP253951: NHBE mock treatment versus infected with SARS-CoV-2 (Series 1): mock;SRX7990866,SRX7990867,SRX7990868: SARS-CoV-2; SRX7990869,SRX7990870,SRX7990871;## 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:
## ..$ SRR11412215: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412216: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412217: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412218: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412219: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412220: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412221: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412222: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412223: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412224: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412225: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412226: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412231: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412232: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412233: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412234: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412235: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412236: int [1:58302] 0 5 1 0 0 0 0 0 0 2 ...
## ..$ SRR11412237: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412238: int [1:58302] 0 3 2 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 20 variables:
## ..$ SRR11412215: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412216: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412217: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412218: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412219: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412220: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412221: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412222: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412223: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412224: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412225: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412226: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412231: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412232: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412233: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412234: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412235: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412236: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412237: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412238: 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:
## ..$ SRR11412215: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "136" ...
## ..$ SRR11412216: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "136" ...
## ..$ SRR11412217: chr [1:30] "SE" "Sanger/Illumina1.9" "57" "137" ...
## ..$ SRR11412218: chr [1:30] "SE" "Sanger/Illumina1.9" "52" "137" ...
## ..$ SRR11412219: chr [1:30] "SE" "Sanger/Illumina1.9" "46" "131" ...
## ..$ SRR11412220: chr [1:30] "SE" "Sanger/Illumina1.9" "42" "131" ...
## ..$ SRR11412221: chr [1:30] "SE" "Sanger/Illumina1.9" "52" "130" ...
## ..$ SRR11412222: chr [1:30] "SE" "Sanger/Illumina1.9" "53" "132" ...
## ..$ SRR11412223: chr [1:30] "SE" "Sanger/Illumina1.9" "48" "121" ...
## ..$ SRR11412224: chr [1:30] "SE" "Sanger/Illumina1.9" "42" "121" ...
## ..$ SRR11412225: chr [1:30] "SE" "Sanger/Illumina1.9" "43" "122" ...
## ..$ SRR11412226: chr [1:30] "SE" "Sanger/Illumina1.9" "43" "121" ...
## ..$ SRR11412231: chr [1:30] "SE" "Sanger/Illumina1.9" "47" "144" ...
## ..$ SRR11412232: chr [1:30] "SE" "Sanger/Illumina1.9" "44" "141" ...
## ..$ SRR11412233: chr [1:30] "SE" "Sanger/Illumina1.9" "44" "144" ...
## ..$ SRR11412234: chr [1:30] "SE" "Sanger/Illumina1.9" "53" "144" ...
## ..$ SRR11412235: chr [1:30] "SE" "Sanger/Illumina1.9" "46" "139" ...
## ..$ SRR11412236: chr [1:30] "SE" "Sanger/Illumina1.9" "47" "137" ...
## ..$ SRR11412237: chr [1:30] "SE" "Sanger/Illumina1.9" "52" "139" ...
## ..$ SRR11412238: chr [1:30] "SE" "Sanger/Illumina1.9" "52" "139" ...
## $ MetadataSummary:'data.frame': 20 obs. of 7 variables:
## ..$ QC_summary : chr [1:20] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:20] "SRX7990866" "SRX7990866" "SRX7990866" "SRX7990866" ...
## ..$ SRS_accession: chr [1:20] "SRS6374419" "SRS6374419" "SRS6374419" "SRS6374419" ...
## ..$ SRP_accession: chr [1:20] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:20] "GSM4432378" "GSM4432378" "GSM4432378" "GSM4432378" ...
## ..$ GEO_series : chr [1:20] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:20] "SRX7990866" "SRX7990866" "SRX7990866" "SRX7990866" ...
## ..$ SRS_accession : chr [1:20] "SRS6374419" "SRS6374419" "SRS6374419" "SRS6374419" ...
## ..$ SRP_accession : chr [1:20] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:20] "GSM4432378" "GSM4432378" "GSM4432378" "GSM4432378" ...
## ..$ GEO_series : chr [1:20] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:20] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:20] "GSM4432378" "GSM4432378" "GSM4432378" "GSM4432378" ...
## ..$ ReleaseDate : chr [1:20] "2020-03-26 16:41:06" "2020-03-26 16:41:06" "2020-03-26 16:41:06" "2020-03-26 16:41:06" ...
## ..$ LoadDate : chr [1:20] "2020-03-25 01:58:30" "2020-03-25 01:59:43" "2020-03-25 01:59:39" "2020-03-25 01:59:57" ...
## ..$ spots : int [1:20] 4260400 4175640 4322242 4245291 4106965 4027775 4144278 4032103 6111163 6020043 ...
## ..$ bases : int [1:20] 558210660 547162776 566041144 555639544 524883325 514317390 529851552 514225167 734468035 723823606 ...
## ..$ spots_with_mates : int [1:20] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:20] 131 131 130 130 127 127 127 127 120 120 ...
## ..$ size_MB : int [1:20] 231 224 219 214 212 205 199 192 296 289 ...
## ..$ AssemblyName : logi [1:20] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:20] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011144/SRR11412215" "https://sra-download.ncbi.nlm.nih.gov/traces/sra61/SRR/011144/SRR11412216" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011144/SRR11412217" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011144/SRR11412218" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:20] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:20] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:20] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:20] 615032 615032 615032 615032 615032 615032 615032 615032 615032 615032 ...
## ..$ Sample : chr [1:20] "SRS6374419" "SRS6374419" "SRS6374419" "SRS6374419" ...
## ..$ BioSample : chr [1:20] "SAMN14444845" "SAMN14444845" "SAMN14444845" "SAMN14444845" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:20] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:20] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:20] "C9643B1011B36CC2CAE79D18E9120F87" "D3A2CE0CDD17532F6157163A3FF456A4" "C06BC457E87BBBC803861FCA11F6CBDD" "DEF377A1149EF3CB5627ACCB8137B344" ...
## ..$ ReadHash : chr [1:20] "D2457CA5524A8D5D14BA65949754A4CD" "3B884D79213D131813C331DC0DBEA21E" "4A4BE0DAD12A14C30DE9021FD3626BC2" "FB641B4BE3336742B17DC01D0525CEA3" ...
## $ 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
## SRP253951: A549 mock treatment versus infected with SARS-CoV-2 (Series 2): mock;SRX7990872,SRX7990873,SRX7990874: SARS-CoV-2; SRX7990875,SRX7990876,SRX7990877;## 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:
## ..$ SRR11412239: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412240: int [1:58302] 0 2 0 0 0 0 0 0 0 1 ...
## ..$ SRR11412241: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412242: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412243: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412244: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412245: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412246: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR11412247: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412248: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412249: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412250: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412255: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412256: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412257: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412258: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412259: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412260: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412261: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412262: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 20 variables:
## ..$ SRR11412239: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412240: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412241: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412242: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412243: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412244: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412245: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412246: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412247: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412248: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412249: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412250: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412255: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412256: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412257: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412258: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412259: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412260: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412261: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412262: 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:
## ..$ SRR11412239: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412240: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412241: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412242: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412243: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412244: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412245: chr [1:30] "SE" "Sanger/Illumina1.9" "75" "151" ...
## ..$ SRR11412246: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412247: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412248: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412249: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412250: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412255: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412256: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412257: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412258: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412259: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412260: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412261: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412262: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## $ MetadataSummary:'data.frame': 20 obs. of 7 variables:
## ..$ QC_summary : chr [1:20] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:20] "SRX7990872" "SRX7990872" "SRX7990872" "SRX7990872" ...
## ..$ SRS_accession: chr [1:20] "SRS6374424" "SRS6374424" "SRS6374424" "SRS6374424" ...
## ..$ SRP_accession: chr [1:20] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:20] "GSM4432384" "GSM4432384" "GSM4432384" "GSM4432384" ...
## ..$ GEO_series : chr [1:20] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:20] "SRX7990872" "SRX7990872" "SRX7990872" "SRX7990872" ...
## ..$ SRS_accession : chr [1:20] "SRS6374424" "SRS6374424" "SRS6374424" "SRS6374424" ...
## ..$ SRP_accession : chr [1:20] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:20] "GSM4432384" "GSM4432384" "GSM4432384" "GSM4432384" ...
## ..$ GEO_series : chr [1:20] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:20] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:20] "GSM4432384" "GSM4432384" "GSM4432384" "GSM4432384" ...
## ..$ ReleaseDate : chr [1:20] "2020-03-26 16:41:06" "2020-03-26 16:41:06" "2020-03-26 16:41:06" "2020-03-26 16:41:06" ...
## ..$ LoadDate : chr [1:20] "2020-03-25 02:00:40" "2020-03-25 02:00:37" "2020-03-25 02:01:09" "2020-03-25 02:01:24" ...
## ..$ spots : int [1:20] 6647150 6606107 6933877 6826811 3628678 3612583 3781064 3722519 2880493 2862323 ...
## ..$ bases : int [1:20] 965357051 959543406 1007515429 991985964 527601116 525324037 550044036 541563810 420723596 418109970 ...
## ..$ spots_with_mates : int [1:20] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:20] 145 145 145 145 145 145 145 145 146 146 ...
## ..$ size_MB : int [1:20] 386 379 376 367 211 207 205 200 168 165 ...
## ..$ AssemblyName : logi [1:20] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:20] "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011144/SRR11412239" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011144/SRR11412240" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011144/SRR11412241" "https://sra-download.ncbi.nlm.nih.gov/traces/sra61/SRR/011144/SRR11412242" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:20] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:20] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:20] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:20] 615032 615032 615032 615032 615032 615032 615032 615032 615032 615032 ...
## ..$ Sample : chr [1:20] "SRS6374424" "SRS6374424" "SRS6374424" "SRS6374424" ...
## ..$ BioSample : chr [1:20] "SAMN14444839" "SAMN14444839" "SAMN14444839" "SAMN14444839" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:20] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:20] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:20] "36D443CEB5A38335A1F781D7CD5DB724" "814B51629CAC2E71EAE7BECB17E51C0B" "D1BE91521563B2BB3AF4FEB7C428834F" "E9ED7CAF520062A4B9CB1EB32CD24359" ...
## ..$ ReadHash : chr [1:20] "D2764365DB2E490BDAB709909BC547E1" "655415D9E83EC4B141DCEDB49127B98C" "03105BF2F24EEF9909A4A3488528CA92" "265C6783BA14A3FAECC81D6C57397647" ...
## $ 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
## SRP253951: A549 mock treatment versus infected with Respiratory syncytial virus (Series 3): mock;SRX7990878,SRX7990879: RSV;SRX7990880,SRX7990881;## 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:
## ..$ SRR11412263: int [1:58302] 0 4 2 0 0 0 0 0 0 0 ...
## ..$ SRR11412264: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412265: int [1:58302] 1 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412266: int [1:58302] 1 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412267: int [1:58302] 0 2 0 0 0 0 0 0 0 1 ...
## ..$ SRR11412268: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412269: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412270: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412271: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412272: int [1:58302] 0 1 3 0 0 0 0 0 0 0 ...
## ..$ SRR11412273: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412274: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412275: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11412276: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412277: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412278: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 16 variables:
## ..$ SRR11412263: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412264: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412265: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412266: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412267: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412268: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412269: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412270: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412271: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412272: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412273: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412274: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412275: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412276: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412277: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412278: 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:
## ..$ SRR11412263: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412264: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412265: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412266: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412267: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412268: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412269: chr [1:30] "SE" "Sanger/Illumina1.9" "57" "151" ...
## ..$ SRR11412270: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412271: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11412272: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11412273: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412274: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412275: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11412276: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11412277: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11412278: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## $ MetadataSummary:'data.frame': 16 obs. of 7 variables:
## ..$ QC_summary : chr [1:16] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:16] "SRX7990878" "SRX7990878" "SRX7990878" "SRX7990878" ...
## ..$ SRS_accession: chr [1:16] "SRS6374428" "SRS6374428" "SRS6374428" "SRS6374428" ...
## ..$ SRP_accession: chr [1:16] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:16] "GSM4432390" "GSM4432390" "GSM4432390" "GSM4432390" ...
## ..$ GEO_series : chr [1:16] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:16] "SRX7990878" "SRX7990878" "SRX7990878" "SRX7990878" ...
## ..$ SRS_accession : chr [1:16] "SRS6374428" "SRS6374428" "SRS6374428" "SRS6374428" ...
## ..$ SRP_accession : chr [1:16] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:16] "GSM4432390" "GSM4432390" "GSM4432390" "GSM4432390" ...
## ..$ GEO_series : chr [1:16] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:16] "GSM4432390" "GSM4432390" "GSM4432390" "GSM4432390" ...
## ..$ ReleaseDate : chr [1:16] "2020-03-26 16:41:06" "2020-03-26 16:41:06" "2020-03-26 16:41:06" "2020-03-26 16:41:06" ...
## ..$ LoadDate : chr [1:16] "2020-03-25 02:02:20" "2020-03-25 02:01:24" "2020-03-25 02:05:10" "2020-03-25 02:01:58" ...
## ..$ spots : int [1:16] 7955076 7855458 8218890 8048208 6466077 6404966 6706893 6578304 2794272 2766068 ...
## ..$ bases : int [1:16] 1147189797 1132977436 1185633130 1161006449 949012516 940110515 984540431 965681408 401040883 397057821 ...
## ..$ spots_with_mates : int [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:16] 144 144 144 144 146 146 146 146 143 143 ...
## ..$ size_MB : int [1:16] 459 448 441 430 377 370 365 355 161 158 ...
## ..$ AssemblyName : logi [1:16] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:16] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011144/SRR11412263" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011144/SRR11412264" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011144/SRR11412265" "https://sra-download.ncbi.nlm.nih.gov/traces/sra61/SRR/011144/SRR11412266" ...
## ..$ 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] "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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:16] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:16] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:16] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:16] 615032 615032 615032 615032 615032 615032 615032 615032 615032 615032 ...
## ..$ Sample : chr [1:16] "SRS6374428" "SRS6374428" "SRS6374428" "SRS6374428" ...
## ..$ BioSample : chr [1:16] "SAMN14444833" "SAMN14444833" "SAMN14444833" "SAMN14444833" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:16] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:16] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:16] "D4161FA82F8501E9B6EF93701283F33D" "BAD7F14520D34B964A34BBDC140C9DB7" "BDB6B32D2B24BD17115076385E2A83E9" "849CB1901024ADE85C4237293466BF55" ...
## ..$ ReadHash : chr [1:16] "A940CB5FD14641FF6E832B03026A9026" "3A4AAC8004AA8B3CC99D7DCEB5F0DE07" "6956ACD30A3EF7A72C8F87D43C88C043" "7275740EBFFF4E2C46C9746445FA1F0E" ...
## $ 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
## SRP253951: A549 mock treatment versus infected with Influenza A virus (Series 4): mock;SRX7990882,SRX7990883: IAV;SRX7990884,SRX7990885;## 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:
## ..$ SRR11412279: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412280: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412281: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412282: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412283: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412284: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412285: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412286: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412287: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412288: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412289: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412290: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412291: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412292: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412293: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412294: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 16 variables:
## ..$ SRR11412279: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412280: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412281: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412282: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412283: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412284: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412285: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412286: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412287: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412288: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412289: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412290: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412291: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412292: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412293: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11412294: 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:
## ..$ SRR11412279: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412280: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412281: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412282: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412283: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412284: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412285: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412286: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11412287: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11412288: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11412289: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11412290: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11412291: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "147" ...
## ..$ SRR11412292: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "149" ...
## ..$ SRR11412293: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "149" ...
## ..$ SRR11412294: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "148" ...
## $ MetadataSummary:'data.frame': 16 obs. of 7 variables:
## ..$ QC_summary : chr [1:16] "FAIL(5)" "FAIL(5)" "FAIL(5)" "FAIL(5)" ...
## ..$ SRX_accession: chr [1:16] "SRX7990882" "SRX7990882" "SRX7990882" "SRX7990882" ...
## ..$ SRS_accession: chr [1:16] "SRS6374433" "SRS6374433" "SRS6374433" "SRS6374433" ...
## ..$ SRP_accession: chr [1:16] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:16] "GSM4432394" "GSM4432394" "GSM4432394" "GSM4432394" ...
## ..$ GEO_series : chr [1:16] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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(5)" "FAIL(5)" "FAIL(5)" "FAIL(5)" ...
## ..$ SRX_accession : chr [1:16] "SRX7990882" "SRX7990882" "SRX7990882" "SRX7990882" ...
## ..$ SRS_accession : chr [1:16] "SRS6374433" "SRS6374433" "SRS6374433" "SRS6374433" ...
## ..$ SRP_accession : chr [1:16] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:16] "GSM4432394" "GSM4432394" "GSM4432394" "GSM4432394" ...
## ..$ GEO_series : chr [1:16] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:16] "GSM4432394" "GSM4432394" "GSM4432394" "GSM4432394" ...
## ..$ ReleaseDate : chr [1:16] "2020-03-26 16:41:07" "2020-03-26 16:41:07" "2020-03-26 16:41:07" "2020-03-26 16:41:07" ...
## ..$ LoadDate : chr [1:16] "2020-03-25 01:58:10" "2020-03-25 01:58:07" "2020-03-25 01:58:07" "2020-03-25 01:58:06" ...
## ..$ spots : int [1:16] 1369515 1350455 1417013 1405918 2773749 2719499 2817721 2792070 3382782 3313587 ...
## ..$ bases : int [1:16] 199745866 196974950 206852005 205250178 385891212 379157694 392349745 388828497 468263147 458855885 ...
## ..$ spots_with_mates : int [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:16] 145 145 145 145 139 139 139 139 138 138 ...
## ..$ size_MB : int [1:16] 76 74 75 74 147 143 142 140 177 171 ...
## ..$ AssemblyName : logi [1:16] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:16] "https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/011144/SRR11412279" "https://sra-download.ncbi.nlm.nih.gov/traces/sra61/SRR/011144/SRR11412280" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011144/SRR11412281" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011144/SRR11412282" ...
## ..$ 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] "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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:16] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:16] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:16] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:16] 615032 615032 615032 615032 615032 615032 615032 615032 615032 615032 ...
## ..$ Sample : chr [1:16] "SRS6374433" "SRS6374433" "SRS6374433" "SRS6374433" ...
## ..$ BioSample : chr [1:16] "SAMN14444829" "SAMN14444829" "SAMN14444829" "SAMN14444829" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:16] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:16] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:16] "29BA98CB92823E4581A083A1E26D73D9" "927BD7456F73E492F5AE7970314EA3EE" "25147562175814B0D6F04A2E0B23B1BA" "767FC42AB151745CA9C1144FB9A07AE5" ...
## ..$ ReadHash : chr [1:16] "29407A08E34345D5BD84F32C58A4A48D" "C41C1101BCFC3839A91AED56B0E801C3" "EE2E8F006B072130490D467842A921F5" "75B602B416F4E1F7432F801953EB190D" ...
## $ absent : chr(0)## SRP253951: A549 mock treatment versus infected with SARS-CoV-2 (Series 5): mock; SRX8089264,SRX8089265,SRX8089266: SARS-COV-2;SRX8089267,SRX8089268, SRX8089269;
## 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:
## ..$ SRR11517675: int [1:58302] 1 4 2 0 0 0 0 0 0 0 ...
## ..$ SRR11517676: int [1:58302] 0 6 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517677: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517678: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11517675: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517676: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517677: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517678: 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:
## ..$ SRR11517675: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "146" ...
## ..$ SRR11517676: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517677: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517678: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8089265" "SRX8089266" "SRX8089267" "SRX8089268"
## ..$ SRS_accession: chr [1:4] "SRS6456134" "SRS6456135" "SRS6456136" "SRS6456137"
## ..$ SRP_accession: chr [1:4] "SRP253951" "SRP253951" "SRP253951" "SRP253951"
## ..$ Sample_name : chr [1:4] "GSM4462337" "GSM4462338" "GSM4462339" "GSM4462340"
## ..$ GEO_series : chr [1:4] "GSE147507" "GSE147507" "GSE147507" "GSE147507"
## ..$ 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" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8089265" "SRX8089266" "SRX8089267" "SRX8089268"
## ..$ SRS_accession : chr [1:4] "SRS6456134" "SRS6456135" "SRS6456136" "SRS6456137"
## ..$ SRP_accession : chr [1:4] "SRP253951" "SRP253951" "SRP253951" "SRP253951"
## ..$ Sample_name : chr [1:4] "GSM4462337" "GSM4462338" "GSM4462339" "GSM4462340"
## ..$ GEO_series : chr [1:4] "GSE147507" "GSE147507" "GSE147507" "GSE147507"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4462337" "GSM4462338" "GSM4462339" "GSM4462340"
## ..$ ReleaseDate : chr [1:4] "2020-04-10 23:37:54" "2020-04-10 22:18:15" "2020-04-10 23:10:39" "2020-04-10 23:08:49"
## ..$ LoadDate : chr [1:4] "2020-04-10 23:20:51" "2020-04-10 21:49:32" "2020-04-10 23:05:22" "2020-04-10 22:45:14"
## ..$ spots : int [1:4] 23809078 22166099 22280277 24949250
## ..$ bases : num [1:4] 3.16e+09 3.06e+09 3.12e+09 3.45e+09
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 132 138 140 138
## ..$ size_MB : int [1:4] 1385 1330 1354 1504
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra58/SRR/011247/SRR11517675" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011247/SRR11517676" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517677" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011247/SRR11517678"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP253951" "SRP253951" "SRP253951" "SRP253951"
## ..$ BioProject : chr [1:4] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032"
## ..$ Study_Pubmed_id : int [1:4] 3 3 3 3
## ..$ ProjectID : int [1:4] 615032 615032 615032 615032
## ..$ Sample : chr [1:4] "SRS6456134" "SRS6456135" "SRS6456136" "SRS6456137"
## ..$ BioSample : chr [1:4] "SAMN14563434" "SAMN14563433" "SAMN14563432" "SAMN14563431"
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "444D9FFE0D2B13383795FA900D74ABCC" "BF1C133CDC510A67E28BBD69E3D5CC4D" "4FA6DBEB1A6B661FF40DA63CF390468E" "DAC3FF5A4D75AC368AACB41C16B03DD1"
## ..$ ReadHash : chr [1:4] "58DED948C53DB2FB16BE872E5B714C5E" "4F1736ABE3E7E2FB7C186E26BC3DBAAE" "1C6D14AA22CEB66907A40AC26178653F" "3A960BAD7979D4191602C492BD85B4CE"
## $ 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
## SRP253951: A549 induced with ACE2 mock treatment versus infected with SARS-CoV-2 (Series 6): mock;SRX8089270,SRX8089271, SRX8089272: SARS-CoV-2;SRX8089273,SRX8089274,SRX8089275;## 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:
## ..$ SRR11517680: int [1:58302] 0 5 3 0 0 0 0 0 0 0 ...
## ..$ SRR11517681: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517741: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517742: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517743: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR11517680: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517681: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517741: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517742: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517743: 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:
## ..$ SRR11517680: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517681: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517741: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517742: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517743: chr [1:30] "SE" "Sanger/Illumina1.9" "53" "150" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "PASS" "WARN(1,5,7)" "FAIL(3,4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession: chr [1:5] "SRX8089270" "SRX8089271" "SRX8089273" "SRX8089274" ...
## ..$ SRS_accession: chr [1:5] "SRS6456138" "SRS6456140" "SRS6456141" "SRS6456143" ...
## ..$ SRP_accession: chr [1:5] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:5] "GSM4462342" "GSM4462343" "GSM4462345" "GSM4462346" ...
## ..$ GEO_series : chr [1:5] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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(1,5,7)" "FAIL(3,4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession : chr [1:5] "SRX8089270" "SRX8089271" "SRX8089273" "SRX8089274" ...
## ..$ SRS_accession : chr [1:5] "SRS6456138" "SRS6456140" "SRS6456141" "SRS6456143" ...
## ..$ SRP_accession : chr [1:5] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:5] "GSM4462342" "GSM4462343" "GSM4462345" "GSM4462346" ...
## ..$ GEO_series : chr [1:5] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM4462342" "GSM4462343" "GSM4462345" "GSM4462346" ...
## ..$ ReleaseDate : chr [1:5] "2020-04-11 00:06:29" "2020-04-10 21:36:30" "2020-04-10 23:27:27" "2020-04-10 22:03:17" ...
## ..$ LoadDate : chr [1:5] "2020-04-11 00:03:11" "2020-04-10 21:25:16" "2020-04-10 22:49:42" "2020-04-10 21:52:35" ...
## ..$ spots : int [1:5] 29164551 2669447 23586566 5720676 4841347
## ..$ bases : num [1:5] 4.17e+09 3.67e+08 3.18e+09 7.74e+08 6.64e+08
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 142 137 134 135 137
## ..$ size_MB : int [1:5] 1802 161 1378 339 287
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/011247/SRR11517680" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011247/SRR11517681" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011247/SRR11517741" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011247/SRR11517742" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:5] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:5] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:5] 3 3 3 3 3
## ..$ ProjectID : int [1:5] 615032 615032 615032 615032 615032
## ..$ Sample : chr [1:5] "SRS6456138" "SRS6456140" "SRS6456141" "SRS6456143" ...
## ..$ BioSample : chr [1:5] "SAMN14563429" "SAMN14563428" "SAMN14563426" "SAMN14563425" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "485C4460A7D05F06D7ACC4A7B6AD6264" "EDC1AD57DAEF877A13829B5D2C31DBDC" "7E01D7DA50E738408B7DE6EC7E0709AB" "B8E59FCD6EECC5A008648FDBD5F66D69" ...
## ..$ ReadHash : chr [1:5] "103D9FBCF466B9A6106C357973A0180F" "30167C84CDD63D9910D0601105BEF6D4" "E1136C9A1CEB5A7A0B082A61D14DC254" "25C9E2ADA407BCC639814893A1AD38E6" ...
## $ absent : chr(0)## SRP253951: Calu3 mock treatment versus infected with SARS-CoV-2 (Series 7): mock;SRX8089276,SRX8089277,SRX8089278: SARS-CoV-2;SRX8089279,SRX8089280,SRX8089281;
## 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:
## ..$ SRR11517744: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517745: int [1:58302] 0 7 9 0 0 0 0 0 0 1 ...
## ..$ SRR11517746: int [1:58302] 0 9 17 0 0 0 0 0 0 11 ...
## ..$ SRR11517747: int [1:58302] 0 13 5 0 0 0 0 0 0 5 ...
## ..$ SRR11517748: int [1:58302] 0 2 6 0 0 0 0 0 0 1 ...
## ..$ SRR11517749: int [1:58302] 0 9 5 0 0 0 0 0 0 4 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11517744: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517745: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517746: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517747: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517748: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517749: 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:
## ..$ SRR11517744: chr [1:30] "SE" "Sanger/Illumina1.9" "44" "149" ...
## ..$ SRR11517745: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517746: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517747: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517748: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517749: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(1,5,7)" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8089276" "SRX8089277" "SRX8089278" "SRX8089279" ...
## ..$ SRS_accession: chr [1:6] "SRS6456146" "SRS6456145" "SRS6456147" "SRS6456148" ...
## ..$ SRP_accession: chr [1:6] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:6] "GSM4462348" "GSM4462349" "GSM4462350" "GSM4462351" ...
## ..$ GEO_series : chr [1:6] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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)" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX8089276" "SRX8089277" "SRX8089278" "SRX8089279" ...
## ..$ SRS_accession : chr [1:6] "SRS6456146" "SRS6456145" "SRS6456147" "SRS6456148" ...
## ..$ SRP_accession : chr [1:6] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:6] "GSM4462348" "GSM4462349" "GSM4462350" "GSM4462351" ...
## ..$ GEO_series : chr [1:6] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4462348" "GSM4462349" "GSM4462350" "GSM4462351" ...
## ..$ ReleaseDate : chr [1:6] "2020-04-10 22:17:37" "2020-04-10 23:08:49" "2020-04-11 00:30:28" "2020-04-10 23:26:19" ...
## ..$ LoadDate : chr [1:6] "2020-04-10 22:15:21" "2020-04-10 22:47:49" "2020-04-10 23:37:15" "2020-04-10 23:05:31" ...
## ..$ spots : int [1:6] 9324151 17436078 37787485 23623325 13583713 28688015
## ..$ bases : num [1:6] 1.26e+09 2.39e+09 5.19e+09 3.23e+09 1.91e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 135 137 137 136 140 134
## ..$ size_MB : int [1:6] 552 1051 2258 1401 827 1681
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/011247/SRR11517744" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517745" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011247/SRR11517746" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011247/SRR11517747" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:6] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 615032 615032 615032 615032 615032 615032
## ..$ Sample : chr [1:6] "SRS6456146" "SRS6456145" "SRS6456147" "SRS6456148" ...
## ..$ BioSample : chr [1:6] "SAMN14563423" "SAMN14563422" "SAMN14563421" "SAMN14563420" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "22507997EE12BC1C081C0F7E50A30468" "187B471B18D415F4ED7E4E14702978CE" "227A6236F53283A7249A87C2AC5DEF9A" "54CAFC03776F256CDB825F6ACDFB86EA" ...
## ..$ ReadHash : chr [1:6] "082612D474428A7107C9B7B00E46D72D" "4E3207B962462BCB6B8B58B3C39E6716" "FFBF88E623D360EC784FD20FD049324E" "30A297023B17E6BED5C47C3BD34F6B91" ...
## $ 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
## SRP253951: A549 mock treatment versus infected with Respiratory syncytial virus ((Series 8): mock;SRX8089282,SRX8089283,SRX8089284: RSV;SRX8089285,SRX8089286,SRX8089287;## 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:
## ..$ SRR11517750: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517751: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517752: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517753: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517754: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517755: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11517750: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517751: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517752: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517753: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517754: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517755: 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:
## ..$ SRR11517750: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517751: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517752: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517753: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517754: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517755: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(5,7)" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8089282" "SRX8089283" "SRX8089284" "SRX8089285" ...
## ..$ SRS_accession: chr [1:6] "SRS6456152" "SRS6456151" "SRS6456153" "SRS6456154" ...
## ..$ SRP_accession: chr [1:6] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:6] "GSM4462354" "GSM4462355" "GSM4462356" "GSM4462357" ...
## ..$ GEO_series : chr [1:6] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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(1,5,7)" "WARN(5,7)" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX8089282" "SRX8089283" "SRX8089284" "SRX8089285" ...
## ..$ SRS_accession : chr [1:6] "SRS6456152" "SRS6456151" "SRS6456153" "SRS6456154" ...
## ..$ SRP_accession : chr [1:6] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:6] "GSM4462354" "GSM4462355" "GSM4462356" "GSM4462357" ...
## ..$ GEO_series : chr [1:6] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4462354" "GSM4462355" "GSM4462356" "GSM4462357" ...
## ..$ ReleaseDate : chr [1:6] "2020-04-10 21:56:15" "2020-04-10 22:02:40" "2020-04-10 22:29:13" "2020-04-10 22:55:34" ...
## ..$ LoadDate : chr [1:6] "2020-04-10 21:52:51" "2020-04-10 21:56:31" "2020-04-10 22:14:06" "2020-04-10 22:34:28" ...
## ..$ spots : int [1:6] 5728818 6459060 11337279 18265188 10113566 17024730
## ..$ bases : num [1:6] 7.96e+08 9.18e+08 1.61e+09 2.61e+09 1.40e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 138 142 142 143 138 140
## ..$ size_MB : int [1:6] 303 342 600 964 520 883
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517750" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517751" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011247/SRR11517752" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011247/SRR11517753" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:6] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 615032 615032 615032 615032 615032 615032
## ..$ Sample : chr [1:6] "SRS6456152" "SRS6456151" "SRS6456153" "SRS6456154" ...
## ..$ BioSample : chr [1:6] "SAMN14563417" "SAMN14563416" "SAMN14563415" "SAMN14563414" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "3637E6C6787B4282563E12D8A38DF387" "C572BC75A2B1BE034FE83BD29CD7F8DC" "7AA63CC58EEA03A82757267A8062DCFF" "DD025E3B855E180DD84ACDBD9B914189" ...
## ..$ ReadHash : chr [1:6] "836F2979E06F44C49C862F55FD3C5CE8" "2DB21310000BCC65C65FC07C4EF6A93A" "1E11437C03897240DA8A137DD8C279FD" "A27A1668E8FB6CDDF7A112DC5C98FEE6" ...
## $ 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
## SRP253951: A549 mock treatment versus infected with Human parainfluenza virus type 3 (HPIV3) (Series 8): mock;SRX8089282,SRX8089283,SRX8089284: HPIV3;SRX8089288,SRX8089289,SRX8089290;## 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:
## ..$ SRR11517750: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517751: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517752: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517756: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517757: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517758: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11517750: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517751: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517752: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517756: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517757: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517758: 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:
## ..$ SRR11517750: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517751: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517752: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517756: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "142" ...
## ..$ SRR11517757: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517758: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "149" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(5,7)" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8089282" "SRX8089283" "SRX8089284" "SRX8089288" ...
## ..$ SRS_accession: chr [1:6] "SRS6456152" "SRS6456151" "SRS6456153" "SRS6456157" ...
## ..$ SRP_accession: chr [1:6] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:6] "GSM4462354" "GSM4462355" "GSM4462356" "GSM4462360" ...
## ..$ GEO_series : chr [1:6] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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(1,5,7)" "WARN(5,7)" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX8089282" "SRX8089283" "SRX8089284" "SRX8089288" ...
## ..$ SRS_accession : chr [1:6] "SRS6456152" "SRS6456151" "SRS6456153" "SRS6456157" ...
## ..$ SRP_accession : chr [1:6] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:6] "GSM4462354" "GSM4462355" "GSM4462356" "GSM4462360" ...
## ..$ GEO_series : chr [1:6] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4462354" "GSM4462355" "GSM4462356" "GSM4462360" ...
## ..$ ReleaseDate : chr [1:6] "2020-04-10 21:56:15" "2020-04-10 22:02:40" "2020-04-10 22:29:13" "2020-04-10 22:47:59" ...
## ..$ LoadDate : chr [1:6] "2020-04-10 21:52:51" "2020-04-10 21:56:31" "2020-04-10 22:14:06" "2020-04-10 22:45:08" ...
## ..$ spots : int [1:6] 5728818 6459060 11337279 22489933 15057066 19109384
## ..$ bases : num [1:6] 7.96e+08 9.18e+08 1.61e+09 2.98e+09 2.17e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 138 142 142 132 144 135
## ..$ size_MB : int [1:6] 303 342 600 1104 805 960
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517750" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517751" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011247/SRR11517752" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517756" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:6] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 615032 615032 615032 615032 615032 615032
## ..$ Sample : chr [1:6] "SRS6456152" "SRS6456151" "SRS6456153" "SRS6456157" ...
## ..$ BioSample : chr [1:6] "SAMN14563417" "SAMN14563416" "SAMN14563415" "SAMN14563452" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "3637E6C6787B4282563E12D8A38DF387" "C572BC75A2B1BE034FE83BD29CD7F8DC" "7AA63CC58EEA03A82757267A8062DCFF" "3ED31303B9A216718CF7EA79FC6E6150" ...
## ..$ ReadHash : chr [1:6] "836F2979E06F44C49C862F55FD3C5CE8" "2DB21310000BCC65C65FC07C4EF6A93A" "1E11437C03897240DA8A137DD8C279FD" "7464B66BD2858A93DC6F25281B614195" ...
## $ 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
## SRP253951: NHBE mock treatment versus infected with Influenza A virus (Series 9): mock;SRX8089291,SRX8089292,SRX8089293,SRX8089294: IAV;SRX8089295,SRX8089296,SRX8089297,SRX8089298;## 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 32 variables:
## ..$ SRR11517759: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517760: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517761: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517762: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517763: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517764: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517765: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR11517766: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517767: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517768: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517769: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517770: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517771: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517772: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517773: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517774: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517775: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517776: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517777: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517778: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517779: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517780: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517781: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517782: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517783: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517784: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517785: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517786: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517787: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517788: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517789: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517790: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 32 variables:
## ..$ SRR11517759: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517760: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517761: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517762: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517763: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517764: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517765: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517766: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517767: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517768: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517769: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517770: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517771: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517772: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517773: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517774: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517775: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517776: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517777: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517778: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517779: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517780: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517781: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517782: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517783: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517784: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517785: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517786: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517787: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517788: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517789: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517790: 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 32 variables:
## ..$ SRR11517759: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517760: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517761: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517762: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517763: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517764: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517765: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517766: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517767: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517768: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517769: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517770: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517771: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517772: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517773: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517774: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517775: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "123" ...
## ..$ SRR11517776: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "123" ...
## ..$ SRR11517777: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "123" ...
## ..$ SRR11517778: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "123" ...
## ..$ SRR11517779: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "130" ...
## ..$ SRR11517780: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "129" ...
## ..$ SRR11517781: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "128" ...
## ..$ SRR11517782: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "130" ...
## ..$ SRR11517783: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "125" ...
## ..$ SRR11517784: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "125" ...
## ..$ SRR11517785: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "125" ...
## ..$ SRR11517786: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "124" ...
## ..$ SRR11517787: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "146" ...
## ..$ SRR11517788: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "146" ...
## ..$ SRR11517789: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "144" ...
## ..$ SRR11517790: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "145" ...
## $ MetadataSummary:'data.frame': 32 obs. of 7 variables:
## ..$ QC_summary : chr [1:32] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:32] "SRX8089291" "SRX8089291" "SRX8089291" "SRX8089291" ...
## ..$ SRS_accession: chr [1:32] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ SRP_accession: chr [1:32] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:32] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ GEO_series : chr [1:32] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:32] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 32 obs. of 52 variables:
## ..$ QC_summary : chr [1:32] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:32] "SRX8089291" "SRX8089291" "SRX8089291" "SRX8089291" ...
## ..$ SRS_accession : chr [1:32] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ SRP_accession : chr [1:32] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:32] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ GEO_series : chr [1:32] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:32] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:32] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ ReleaseDate : chr [1:32] "2020-04-10 21:47:44" "2020-04-10 21:53:49" "2020-04-10 21:47:44" "2020-04-10 21:47:44" ...
## ..$ LoadDate : chr [1:32] "2020-04-10 21:44:40" "2020-04-10 21:45:51" "2020-04-10 21:45:17" "2020-04-10 21:45:29" ...
## ..$ spots : int [1:32] 1539573 1574964 1509652 1501003 1600408 1638204 1569150 1560442 2032190 2093577 ...
## ..$ bases : int [1:32] 219724797 224796998 215324869 214050327 229121017 234506827 224547715 223239422 286304133 294951515 ...
## ..$ spots_with_mates : int [1:32] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:32] 142 142 142 142 143 143 143 143 140 140 ...
## ..$ size_MB : int [1:32] 74 75 72 72 77 78 75 75 129 132 ...
## ..$ AssemblyName : logi [1:32] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:32] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517759" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011247/SRR11517760" "https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/011247/SRR11517761" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011247/SRR11517762" ...
## ..$ LibraryName : logi [1:32] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:32] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:32] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:32] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:32] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:32] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:32] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:32] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:32] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:32] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:32] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:32] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:32] 615032 615032 615032 615032 615032 615032 615032 615032 615032 615032 ...
## ..$ Sample : chr [1:32] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ BioSample : chr [1:32] "SAMN14563449" "SAMN14563449" "SAMN14563449" "SAMN14563449" ...
## ..$ SampleType : chr [1:32] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:32] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:32] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:32] NA NA NA NA NA NA ...
## ..$ source : logi [1:32] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:32] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:32] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:32] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:32] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:32] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:32] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:32] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:32] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:32] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:32] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:32] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:32] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:32] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:32] "A70B242F48103DC1C2692B69C658A9FB" "3222B2E6E2C6D63B50902C9A7AA2A4CD" "5903E40EBB238FA4D00BA30E559CB62E" "082AC84BB2B86740962F7ABE4985815F" ...
## ..$ ReadHash : chr [1:32] "E17746DEBBCE43851F66E0EB64A96755" "8A7ABF850A8A88EF5765DAD07350E467" "2B5DE309BDB33C805403EF445F581180" "246B80AB0A5871FDE89C05CEE3E31FEC" ...
## $ 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
## SRP253951: NHBE mock treatment versus infected with Influenza A virus lacking NS1 (Series 9): mock;SRX8089291,SRX8089292,SRX8089293,SRX8089294: IAVdSN1;SRX8089299,SRX8089300,SRX8089301,SRX8089302; 12 hrs (time afer treatment)## 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 32 variables:
## ..$ SRR11517759: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517760: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517761: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517762: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517763: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517764: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517765: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR11517766: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517767: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517768: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517769: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517770: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517771: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517772: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517773: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517774: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517791: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517792: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517793: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517794: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517795: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517796: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517797: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517798: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517799: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517800: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517801: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517802: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517803: int [1:58302] 0 2 2 0 0 0 0 0 0 0 ...
## ..$ SRR11517804: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517805: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517806: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 32 variables:
## ..$ SRR11517759: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517760: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517761: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517762: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517763: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517764: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517765: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517766: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517767: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517768: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517769: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517770: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517771: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517772: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517773: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517774: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517791: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517792: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517793: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517794: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517795: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517796: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517797: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517798: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517799: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517800: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517801: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517802: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517803: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517804: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517805: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517806: 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 32 variables:
## ..$ SRR11517759: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517760: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517761: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517762: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517763: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517764: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517765: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517766: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517767: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517768: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517769: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517770: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517771: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517772: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517773: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517774: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517791: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517792: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517793: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517794: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517795: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517796: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517797: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517798: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517799: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "137" ...
## ..$ SRR11517800: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "135" ...
## ..$ SRR11517801: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "134" ...
## ..$ SRR11517802: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "136" ...
## ..$ SRR11517803: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "137" ...
## ..$ SRR11517804: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "136" ...
## ..$ SRR11517805: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "136" ...
## ..$ SRR11517806: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "138" ...
## $ MetadataSummary:'data.frame': 32 obs. of 7 variables:
## ..$ QC_summary : chr [1:32] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:32] "SRX8089291" "SRX8089291" "SRX8089291" "SRX8089291" ...
## ..$ SRS_accession: chr [1:32] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ SRP_accession: chr [1:32] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:32] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ GEO_series : chr [1:32] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:32] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 32 obs. of 52 variables:
## ..$ QC_summary : chr [1:32] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:32] "SRX8089291" "SRX8089291" "SRX8089291" "SRX8089291" ...
## ..$ SRS_accession : chr [1:32] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ SRP_accession : chr [1:32] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:32] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ GEO_series : chr [1:32] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:32] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:32] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ ReleaseDate : chr [1:32] "2020-04-10 21:47:44" "2020-04-10 21:53:49" "2020-04-10 21:47:44" "2020-04-10 21:47:44" ...
## ..$ LoadDate : chr [1:32] "2020-04-10 21:44:40" "2020-04-10 21:45:51" "2020-04-10 21:45:17" "2020-04-10 21:45:29" ...
## ..$ spots : int [1:32] 1539573 1574964 1509652 1501003 1600408 1638204 1569150 1560442 2032190 2093577 ...
## ..$ bases : int [1:32] 219724797 224796998 215324869 214050327 229121017 234506827 224547715 223239422 286304133 294951515 ...
## ..$ spots_with_mates : int [1:32] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:32] 142 142 142 142 143 143 143 143 140 140 ...
## ..$ size_MB : int [1:32] 74 75 72 72 77 78 75 75 129 132 ...
## ..$ AssemblyName : logi [1:32] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:32] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517759" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011247/SRR11517760" "https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/011247/SRR11517761" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011247/SRR11517762" ...
## ..$ LibraryName : logi [1:32] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:32] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:32] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:32] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:32] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:32] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:32] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:32] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:32] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:32] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:32] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:32] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:32] 615032 615032 615032 615032 615032 615032 615032 615032 615032 615032 ...
## ..$ Sample : chr [1:32] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ BioSample : chr [1:32] "SAMN14563449" "SAMN14563449" "SAMN14563449" "SAMN14563449" ...
## ..$ SampleType : chr [1:32] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:32] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:32] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:32] NA NA NA NA NA NA ...
## ..$ source : logi [1:32] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:32] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:32] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:32] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:32] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:32] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:32] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:32] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:32] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:32] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:32] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:32] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:32] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:32] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:32] "A70B242F48103DC1C2692B69C658A9FB" "3222B2E6E2C6D63B50902C9A7AA2A4CD" "5903E40EBB238FA4D00BA30E559CB62E" "082AC84BB2B86740962F7ABE4985815F" ...
## ..$ ReadHash : chr [1:32] "E17746DEBBCE43851F66E0EB64A96755" "8A7ABF850A8A88EF5765DAD07350E467" "2B5DE309BDB33C805403EF445F581180" "246B80AB0A5871FDE89C05CEE3E31FEC" ...
## $ 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
## SRP253951: NHBE mock treatment versus interferon beta (IFNB) treatment (Series 9): mock;SRX8089291,SRX8089292,SRX8089293,SRX8089294: IFNB;SRX8089303,SRX8089304; 4 hrs (time after treatment)## 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:
## ..$ SRR11517759: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517760: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517761: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517762: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517763: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517764: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517765: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR11517766: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517767: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517768: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517769: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517770: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517771: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517772: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517773: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517774: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517807: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517808: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517809: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR11517810: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517811: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517812: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517813: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517814: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 24 variables:
## ..$ SRR11517759: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517760: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517761: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517762: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517763: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517764: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517765: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517766: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517767: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517768: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517769: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517770: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517771: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517772: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517773: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517774: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517807: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517808: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517809: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517810: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517811: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517812: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517813: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517814: 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:
## ..$ SRR11517759: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517760: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517761: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517762: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517763: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517764: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517765: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517766: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517767: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517768: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517769: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517770: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517771: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517772: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517773: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517774: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517807: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517808: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517809: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517810: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517811: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517812: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517813: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517814: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## $ MetadataSummary:'data.frame': 24 obs. of 7 variables:
## ..$ QC_summary : chr [1:24] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:24] "SRX8089291" "SRX8089291" "SRX8089291" "SRX8089291" ...
## ..$ SRS_accession: chr [1:24] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ SRP_accession: chr [1:24] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:24] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ GEO_series : chr [1:24] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:24] "SRX8089291" "SRX8089291" "SRX8089291" "SRX8089291" ...
## ..$ SRS_accession : chr [1:24] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ SRP_accession : chr [1:24] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:24] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ GEO_series : chr [1:24] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:24] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:24] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ ReleaseDate : chr [1:24] "2020-04-10 21:47:44" "2020-04-10 21:53:49" "2020-04-10 21:47:44" "2020-04-10 21:47:44" ...
## ..$ LoadDate : chr [1:24] "2020-04-10 21:44:40" "2020-04-10 21:45:51" "2020-04-10 21:45:17" "2020-04-10 21:45:29" ...
## ..$ spots : int [1:24] 1539573 1574964 1509652 1501003 1600408 1638204 1569150 1560442 2032190 2093577 ...
## ..$ bases : int [1:24] 219724797 224796998 215324869 214050327 229121017 234506827 224547715 223239422 286304133 294951515 ...
## ..$ spots_with_mates : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:24] 142 142 142 142 143 143 143 143 140 140 ...
## ..$ size_MB : int [1:24] 74 75 72 72 77 78 75 75 129 132 ...
## ..$ AssemblyName : logi [1:24] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:24] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517759" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011247/SRR11517760" "https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/011247/SRR11517761" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011247/SRR11517762" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:24] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:24] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:24] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:24] 615032 615032 615032 615032 615032 615032 615032 615032 615032 615032 ...
## ..$ Sample : chr [1:24] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ BioSample : chr [1:24] "SAMN14563449" "SAMN14563449" "SAMN14563449" "SAMN14563449" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:24] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:24] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:24] "A70B242F48103DC1C2692B69C658A9FB" "3222B2E6E2C6D63B50902C9A7AA2A4CD" "5903E40EBB238FA4D00BA30E559CB62E" "082AC84BB2B86740962F7ABE4985815F" ...
## ..$ ReadHash : chr [1:24] "E17746DEBBCE43851F66E0EB64A96755" "8A7ABF850A8A88EF5765DAD07350E467" "2B5DE309BDB33C805403EF445F581180" "246B80AB0A5871FDE89C05CEE3E31FEC" ...
## $ 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
## SRP253951: NHBE mock treatment versus nterferon beta (IFNB) treatment (Series 9): mock;SRX8089291,SRX8089292,SRX8089293,SRX8089294: IFNB;SRX8089305,SRX8089306; 6 hrs (time after treatment)## 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:
## ..$ SRR11517759: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517760: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517761: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517762: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517763: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517764: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517765: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR11517766: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517767: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517768: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517769: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517770: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517771: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517772: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517773: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517774: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517815: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517816: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517817: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517818: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517819: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517820: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517821: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517822: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 24 variables:
## ..$ SRR11517759: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517760: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517761: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517762: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517763: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517764: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517765: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517766: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517767: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517768: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517769: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517770: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517771: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517772: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517773: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517774: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517815: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517816: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517817: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517818: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517819: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517820: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517821: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517822: 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:
## ..$ SRR11517759: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517760: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517761: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517762: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517763: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517764: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517765: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517766: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517767: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517768: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517769: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517770: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517771: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517772: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517773: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517774: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517815: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517816: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517817: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517818: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517819: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517820: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517821: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517822: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## $ MetadataSummary:'data.frame': 24 obs. of 7 variables:
## ..$ QC_summary : chr [1:24] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:24] "SRX8089291" "SRX8089291" "SRX8089291" "SRX8089291" ...
## ..$ SRS_accession: chr [1:24] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ SRP_accession: chr [1:24] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:24] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ GEO_series : chr [1:24] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:24] "SRX8089291" "SRX8089291" "SRX8089291" "SRX8089291" ...
## ..$ SRS_accession : chr [1:24] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ SRP_accession : chr [1:24] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:24] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ GEO_series : chr [1:24] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:24] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:24] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ ReleaseDate : chr [1:24] "2020-04-10 21:47:44" "2020-04-10 21:53:49" "2020-04-10 21:47:44" "2020-04-10 21:47:44" ...
## ..$ LoadDate : chr [1:24] "2020-04-10 21:44:40" "2020-04-10 21:45:51" "2020-04-10 21:45:17" "2020-04-10 21:45:29" ...
## ..$ spots : int [1:24] 1539573 1574964 1509652 1501003 1600408 1638204 1569150 1560442 2032190 2093577 ...
## ..$ bases : int [1:24] 219724797 224796998 215324869 214050327 229121017 234506827 224547715 223239422 286304133 294951515 ...
## ..$ spots_with_mates : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:24] 142 142 142 142 143 143 143 143 140 140 ...
## ..$ size_MB : int [1:24] 74 75 72 72 77 78 75 75 129 132 ...
## ..$ AssemblyName : logi [1:24] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:24] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517759" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011247/SRR11517760" "https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/011247/SRR11517761" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011247/SRR11517762" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:24] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:24] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:24] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:24] 615032 615032 615032 615032 615032 615032 615032 615032 615032 615032 ...
## ..$ Sample : chr [1:24] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ BioSample : chr [1:24] "SAMN14563449" "SAMN14563449" "SAMN14563449" "SAMN14563449" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:24] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:24] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:24] "A70B242F48103DC1C2692B69C658A9FB" "3222B2E6E2C6D63B50902C9A7AA2A4CD" "5903E40EBB238FA4D00BA30E559CB62E" "082AC84BB2B86740962F7ABE4985815F" ...
## ..$ ReadHash : chr [1:24] "E17746DEBBCE43851F66E0EB64A96755" "8A7ABF850A8A88EF5765DAD07350E467" "2B5DE309BDB33C805403EF445F581180" "246B80AB0A5871FDE89C05CEE3E31FEC" ...
## $ 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
## SRP253951: NHBE mock treatment versus interferon beta (IFNB) treatment (Series 9): mock;SRX8089291,SRX8089292,SRX8089293,SRX8089294: IFNB;SRX8089307,SRX8089308; 12 hrs (time after treatment)## 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:
## ..$ SRR11517759: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517760: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517761: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517762: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517763: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517764: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517765: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR11517766: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517767: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517768: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517769: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517770: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11517771: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517772: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517773: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517774: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517823: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517824: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517825: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517826: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517827: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517828: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517829: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517830: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 24 variables:
## ..$ SRR11517759: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517760: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517761: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517762: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517763: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517764: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517765: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517766: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517767: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517768: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517769: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517770: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517771: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517772: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517773: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517774: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517823: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517824: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517825: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517826: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517827: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517828: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517829: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11517830: 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:
## ..$ SRR11517759: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517760: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517761: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517762: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517763: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517764: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517765: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517766: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517767: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517768: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517769: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517770: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517771: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517772: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517773: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517774: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "150" ...
## ..$ SRR11517823: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517824: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517825: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517826: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517827: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517828: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517829: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## ..$ SRR11517830: chr [1:30] "SE" "Sanger/Illumina1.9" "35" "151" ...
## $ MetadataSummary:'data.frame': 24 obs. of 7 variables:
## ..$ QC_summary : chr [1:24] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:24] "SRX8089291" "SRX8089291" "SRX8089291" "SRX8089291" ...
## ..$ SRS_accession: chr [1:24] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ SRP_accession: chr [1:24] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:24] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ GEO_series : chr [1:24] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ 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(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:24] "SRX8089291" "SRX8089291" "SRX8089291" "SRX8089291" ...
## ..$ SRS_accession : chr [1:24] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ SRP_accession : chr [1:24] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ Sample_name : chr [1:24] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ GEO_series : chr [1:24] "GSE147507" "GSE147507" "GSE147507" "GSE147507" ...
## ..$ Library_name : logi [1:24] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:24] "GSM4462363" "GSM4462363" "GSM4462363" "GSM4462363" ...
## ..$ ReleaseDate : chr [1:24] "2020-04-10 21:47:44" "2020-04-10 21:53:49" "2020-04-10 21:47:44" "2020-04-10 21:47:44" ...
## ..$ LoadDate : chr [1:24] "2020-04-10 21:44:40" "2020-04-10 21:45:51" "2020-04-10 21:45:17" "2020-04-10 21:45:29" ...
## ..$ spots : int [1:24] 1539573 1574964 1509652 1501003 1600408 1638204 1569150 1560442 2032190 2093577 ...
## ..$ bases : int [1:24] 219724797 224796998 215324869 214050327 229121017 234506827 224547715 223239422 286304133 294951515 ...
## ..$ spots_with_mates : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:24] 142 142 142 142 143 143 143 143 140 140 ...
## ..$ size_MB : int [1:24] 74 75 72 72 77 78 75 75 129 132 ...
## ..$ AssemblyName : logi [1:24] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:24] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011247/SRR11517759" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011247/SRR11517760" "https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/011247/SRR11517761" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011247/SRR11517762" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:24] "SRP253951" "SRP253951" "SRP253951" "SRP253951" ...
## ..$ BioProject : chr [1:24] "PRJNA615032" "PRJNA615032" "PRJNA615032" "PRJNA615032" ...
## ..$ Study_Pubmed_id : int [1:24] 3 3 3 3 3 3 3 3 3 3 ...
## ..$ ProjectID : int [1:24] 615032 615032 615032 615032 615032 615032 615032 615032 615032 615032 ...
## ..$ Sample : chr [1:24] "SRS6456159" "SRS6456159" "SRS6456159" "SRS6456159" ...
## ..$ BioSample : chr [1:24] "SAMN14563449" "SAMN14563449" "SAMN14563449" "SAMN14563449" ...
## ..$ 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] "SRA1059108" "SRA1059108" "SRA1059108" "SRA1059108" ...
## ..$ dbgap_study_accession: logi [1:24] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:24] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:24] "A70B242F48103DC1C2692B69C658A9FB" "3222B2E6E2C6D63B50902C9A7AA2A4CD" "5903E40EBB238FA4D00BA30E559CB62E" "082AC84BB2B86740962F7ABE4985815F" ...
## ..$ ReadHash : chr [1:24] "E17746DEBBCE43851F66E0EB64A96755" "8A7ABF850A8A88EF5765DAD07350E467" "2B5DE309BDB33C805403EF445F581180" "246B80AB0A5871FDE89C05CEE3E31FEC" ...
## $ 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
## SRP253279: high binding to the RBD of the S protein versus low binding to the RBD of the S protein (fragments A and B): high binding RBD;SRX7950378,SRX7950380: low binding RBD;SRX7950382,SRX7950384;## 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:
## ..$ SRR11348464: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11348466: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11348468: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11348470: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11348464: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11348466: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11348468: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11348470: 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:
## ..$ SRR11348464: chr [1:30] "PE" "Sanger/Illumina1.9" "250" "250" ...
## ..$ SRR11348466: chr [1:30] "PE" "Sanger/Illumina1.9" "250" "250" ...
## ..$ SRR11348468: chr [1:30] "PE" "Sanger/Illumina1.9" "250" "250" ...
## ..$ SRR11348470: chr [1:30] "PE" "Sanger/Illumina1.9" "250" "250" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)"
## ..$ SRX_accession: chr [1:4] "SRX7950378" "SRX7950380" "SRX7950382" "SRX7950384"
## ..$ SRS_accession: chr [1:4] "SRS6337048" "SRS6337049" "SRS6337052" "SRS6337054"
## ..$ SRP_accession: chr [1:4] "SRP253279" "SRP253279" "SRP253279" "SRP253279"
## ..$ Sample_name : chr [1:4] "GSM4420178" "GSM4420180" "GSM4420182" "GSM4420184"
## ..$ GEO_series : chr [1:4] "GSE147194" "GSE147194" "GSE147194" "GSE147194"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)"
## ..$ SRX_accession : chr [1:4] "SRX7950378" "SRX7950380" "SRX7950382" "SRX7950384"
## ..$ SRS_accession : chr [1:4] "SRS6337048" "SRS6337049" "SRS6337052" "SRS6337054"
## ..$ SRP_accession : chr [1:4] "SRP253279" "SRP253279" "SRP253279" "SRP253279"
## ..$ Sample_name : chr [1:4] "GSM4420178" "GSM4420180" "GSM4420182" "GSM4420184"
## ..$ GEO_series : chr [1:4] "GSE147194" "GSE147194" "GSE147194" "GSE147194"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4420178" "GSM4420180" "GSM4420182" "GSM4420184"
## ..$ ReleaseDate : chr [1:4] "2020-03-20 16:28:34" "2020-03-20 16:28:34" "2020-03-20 16:28:34" "2020-03-20 16:28:34"
## ..$ LoadDate : chr [1:4] "2020-03-19 03:04:36" "2020-03-20 07:46:38" "2020-03-19 12:05:23" "2020-03-19 03:48:10"
## ..$ spots : int [1:4] 31124867 39010249 30242522 34375482
## ..$ bases : num [1:4] 1.56e+10 1.95e+10 1.51e+10 1.72e+10
## ..$ spots_with_mates : int [1:4] 31124867 39010249 30242522 34375482
## ..$ avgLength : int [1:4] 500 500 500 500
## ..$ size_MB : int [1:4] 4280 5325 4124 4667
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra61/SRR/011082/SRR11348464" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011082/SRR11348466" "https://sra-download.ncbi.nlm.nih.gov/traces/sra61/SRR/011082/SRR11348468" "https://sra-download.ncbi.nlm.nih.gov/traces/sra61/SRR/011082/SRR11348470"
## ..$ LibraryName : logi [1:4] NA NA NA NA
## ..$ LibraryStrategy : chr [1:4] "OTHER" "OTHER" "OTHER" "OTHER"
## ..$ LibrarySelection : chr [1:4] "other" "other" "other" "other"
## ..$ LibrarySource : chr [1:4] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr [1:4] "PAIRED" "PAIRED" "PAIRED" "PAIRED"
## ..$ 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 NovaSeq 6000" "Illumina NovaSeq 6000" "Illumina NovaSeq 6000" "Illumina NovaSeq 6000"
## ..$ SRAStudy : chr [1:4] "SRP253279" "SRP253279" "SRP253279" "SRP253279"
## ..$ BioProject : chr [1:4] "PRJNA613297" "PRJNA613297" "PRJNA613297" "PRJNA613297"
## ..$ Study_Pubmed_id : int [1:4] 3 3 3 3
## ..$ ProjectID : int [1:4] 613297 613297 613297 613297
## ..$ Sample : chr [1:4] "SRS6337048" "SRS6337049" "SRS6337052" "SRS6337054"
## ..$ BioSample : chr [1:4] "SAMN14400472" "SAMN14400470" "SAMN14400468" "SAMN14400465"
## ..$ 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] "SRA1056472" "SRA1056472" "SRA1056472" "SRA1056472"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "D42C0F938D14D55DA0EA33F4BDCA13D8" "779EE7789FFB040147E938C65E05F977" "7CC8C6693BDAE03009C3E8029BBA226B" "C396ECCF1FC794730834F5FF4E5679B7"
## ..$ ReadHash : chr [1:4] "3A53148FD9D96407F90BED26877E85A3" "6A2E1E195B3A802ECDCCC3626F9A2363" "C32FA3AABB7B640E0D10A8167C9B51ED" "033D10C135BFEC8FE83DD6AA575E972E"
## $ absent : chr(0)## SRP253279: high binding to the RBD of the S protein versus low binding to the RBD of the S protein (fragments C, D and E):high binding RBD;SRX7950379,SRX7950381: low binding RBD; SRX7950383,SRX7950385;
## 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:
## ..$ SRR11348465: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11348467: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11348471: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 3 variables:
## ..$ SRR11348465: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11348467: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11348471: 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:
## ..$ SRR11348465: chr [1:30] "PE" "Sanger/Illumina1.9" "250" "250" ...
## ..$ SRR11348467: chr [1:30] "PE" "Sanger/Illumina1.9" "250" "250" ...
## ..$ SRR11348471: chr [1:30] "PE" "Sanger/Illumina1.9" "250" "250" ...
## $ MetadataSummary:'data.frame': 3 obs. of 7 variables:
## ..$ QC_summary : chr [1:3] "WARN(8)" "WARN(8)" "WARN(8)"
## ..$ SRX_accession: chr [1:3] "SRX7950379" "SRX7950381" "SRX7950385"
## ..$ SRS_accession: chr [1:3] "SRS6337050" "SRS6337051" "SRS6337055"
## ..$ SRP_accession: chr [1:3] "SRP253279" "SRP253279" "SRP253279"
## ..$ Sample_name : chr [1:3] "GSM4420179" "GSM4420181" "GSM4420185"
## ..$ GEO_series : chr [1:3] "GSE147194" "GSE147194" "GSE147194"
## ..$ Library_name : logi [1:3] NA NA NA
## $ MetadataFull :'data.frame': 3 obs. of 52 variables:
## ..$ QC_summary : chr [1:3] "WARN(8)" "WARN(8)" "WARN(8)"
## ..$ SRX_accession : chr [1:3] "SRX7950379" "SRX7950381" "SRX7950385"
## ..$ SRS_accession : chr [1:3] "SRS6337050" "SRS6337051" "SRS6337055"
## ..$ SRP_accession : chr [1:3] "SRP253279" "SRP253279" "SRP253279"
## ..$ Sample_name : chr [1:3] "GSM4420179" "GSM4420181" "GSM4420185"
## ..$ GEO_series : chr [1:3] "GSE147194" "GSE147194" "GSE147194"
## ..$ Library_name : logi [1:3] NA NA NA
## ..$ SampleName : chr [1:3] "GSM4420179" "GSM4420181" "GSM4420185"
## ..$ ReleaseDate : chr [1:3] "2020-03-20 16:28:34" "2020-03-20 16:28:34" "2020-03-20 16:28:34"
## ..$ LoadDate : chr [1:3] "2020-03-19 03:10:40" "2020-03-20 07:20:37" "2020-03-19 04:03:48"
## ..$ spots : int [1:3] 44714409 44313550 50370595
## ..$ bases : num [1:3] 2.24e+10 2.22e+10 2.52e+10
## ..$ spots_with_mates : int [1:3] 44714409 44313550 50370595
## ..$ avgLength : int [1:3] 500 500 500
## ..$ size_MB : int [1:3] 5831 5789 6682
## ..$ AssemblyName : logi [1:3] NA NA NA
## ..$ download_path : chr [1:3] "https://sra-download.ncbi.nlm.nih.gov/traces/sra52/SRR/011082/SRR11348465" "https://sra-download.ncbi.nlm.nih.gov/traces/sra58/SRR/011082/SRR11348467" "https://sra-download.ncbi.nlm.nih.gov/traces/sra52/SRR/011082/SRR11348471"
## ..$ LibraryName : logi [1:3] NA NA NA
## ..$ LibraryStrategy : chr [1:3] "OTHER" "OTHER" "OTHER"
## ..$ LibrarySelection : chr [1:3] "other" "other" "other"
## ..$ 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 NovaSeq 6000" "Illumina NovaSeq 6000" "Illumina NovaSeq 6000"
## ..$ SRAStudy : chr [1:3] "SRP253279" "SRP253279" "SRP253279"
## ..$ BioProject : chr [1:3] "PRJNA613297" "PRJNA613297" "PRJNA613297"
## ..$ Study_Pubmed_id : int [1:3] 3 3 3
## ..$ ProjectID : int [1:3] 613297 613297 613297
## ..$ Sample : chr [1:3] "SRS6337050" "SRS6337051" "SRS6337055"
## ..$ BioSample : chr [1:3] "SAMN14400471" "SAMN14400469" "SAMN14400464"
## ..$ 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] "SRA1056472" "SRA1056472" "SRA1056472"
## ..$ dbgap_study_accession: logi [1:3] NA NA NA
## ..$ Consent : chr [1:3] "public" "public" "public"
## ..$ RunHash : chr [1:3] "FFF4225EF4A13F08FBF0600F305F3363" "A24D1828005849CE0E318CBB6396692B" "55774EC0412A74380D19FBE17EA323C6"
## ..$ ReadHash : chr [1:3] "CADA9E45A68C5A40243754A1E6090C9B" "185C1EE21FDE09DE0065FF207CC8E659" "F142CB7F47AC1E27CE304ABE0D3A5433"
## $ absent : chr(0)## SRP256479: H1299 cells mock treatment versus infected with SARS-CoV-1 36 hours post infection: mock;SRX8119839,SRX8119840: SARS-CoV-1;SRX8119847,SRX8119848;
## 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:
## ..$ SRR11549937: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549945: int [1:58302] 0 0 3 0 0 0 0 0 0 0 ...
## ..$ SRR11549946: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549937: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549945: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549946: 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:
## ..$ SRR11549937: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549938: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549945: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549946: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119839" "SRX8119840" "SRX8119847" "SRX8119848"
## ..$ SRS_accession: chr [1:4] "SRS6484444" "SRS6484445" "SRS6484452" "SRS6484453"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477854" "GSM4477855" "GSM4477862" "GSM4477863"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ 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" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119839" "SRX8119840" "SRX8119847" "SRX8119848"
## ..$ SRS_accession : chr [1:4] "SRS6484444" "SRS6484445" "SRS6484452" "SRS6484453"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477854" "GSM4477855" "GSM4477862" "GSM4477863"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477854" "GSM4477855" "GSM4477862" "GSM4477863"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01"
## ..$ LoadDate : chr [1:4] "2020-04-15 13:55:51" "2020-04-15 13:58:03" "2020-04-15 14:07:55" "2020-04-15 14:01:50"
## ..$ spots : int [1:4] 13925507 18362063 33321040 17051802
## ..$ bases : num [1:4] 1.06e+09 1.40e+09 2.53e+09 1.30e+09
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 372 473 861 441
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011279/SRR11549937" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011279/SRR11549938" "https://sra-download.ncbi.nlm.nih.gov/traces/sra80/SRR/011279/SRR11549945" "https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRR/011279/SRR11549946"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484444" "SRS6484445" "SRS6484452" "SRS6484453"
## ..$ BioSample : chr [1:4] "SAMN14602092" "SAMN14602091" "SAMN14602132" "SAMN14602131"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "7EE11172BCBEEA2FA9B8C1E9FF2FB9ED" "6755414BE495BC3895B5A8FB4D7B25C7" "742AE0110715564F10CA450D8E1CA712" "1E74B0F0CA7F13DF4F18C34572808B39"
## ..$ ReadHash : chr [1:4] "0F923CF827EB5EE79B4A2CB570D33771" "A44DEF049D06B80DBC4358EC788258E8" "771F880AE5E2ED152C531ADD79C9995D" "64F62439116545FDE04F1A47FEB9C6EA"
## $ 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
## SRP256479: H1299 cells mock treatment versus infected with SARS-CoV-2 36 hours post infection: mock;SRX8119839,SRX8119840: SARS-CoV-2;SRX8119855,SRX8119856;## 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:
## ..$ SRR11549937: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549953: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549954: int [1:58302] 1 2 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549937: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549953: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549954: 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:
## ..$ SRR11549937: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549938: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549953: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549954: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119839" "SRX8119840" "SRX8119855" "SRX8119856"
## ..$ SRS_accession: chr [1:4] "SRS6484444" "SRS6484445" "SRS6484460" "SRS6484461"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477854" "GSM4477855" "GSM4477870" "GSM4477871"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ 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" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119839" "SRX8119840" "SRX8119855" "SRX8119856"
## ..$ SRS_accession : chr [1:4] "SRS6484444" "SRS6484445" "SRS6484460" "SRS6484461"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477854" "GSM4477855" "GSM4477870" "GSM4477871"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477854" "GSM4477855" "GSM4477870" "GSM4477871"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:02" "2020-05-05 09:32:02"
## ..$ LoadDate : chr [1:4] "2020-04-15 13:55:51" "2020-04-15 13:58:03" "2020-04-15 14:03:55" "2020-04-15 14:01:54"
## ..$ spots : int [1:4] 13925507 18362063 19856846 15693254
## ..$ bases : int [1:4] 1058338532 1395516788 1509120296 1192687304
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 372 473 523 403
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011279/SRR11549937" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011279/SRR11549938" "https://sra-download.ncbi.nlm.nih.gov/traces/sra70/SRR/011279/SRR11549953" "https://sra-download.ncbi.nlm.nih.gov/traces/sra66/SRR/011279/SRR11549954"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484444" "SRS6484445" "SRS6484460" "SRS6484461"
## ..$ BioSample : chr [1:4] "SAMN14602092" "SAMN14602091" "SAMN14602124" "SAMN14602123"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "7EE11172BCBEEA2FA9B8C1E9FF2FB9ED" "6755414BE495BC3895B5A8FB4D7B25C7" "DDB021B7E1CB73B68FA323151D5945BB" "87A32D3F841CAB0837029D374EEEA565"
## ..$ ReadHash : chr [1:4] "0F923CF827EB5EE79B4A2CB570D33771" "A44DEF049D06B80DBC4358EC788258E8" "988B6C08CFC9CA1A010BADA164A7BF07" "1C23C9CC59822F08B143E389D28053B4"
## $ 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
## SRP256479: H1299 cells mock treatment versus infected with SARS-CoV-1 4 hours post infection: mock;SRX8119841,SRX8119842: SARS-CoV-1;SRX8119849,SRX8119850;## 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:
## ..$ SRR11549939: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549947: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549948: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549939: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549947: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549948: 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:
## ..$ SRR11549939: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549940: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549947: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549948: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119841" "SRX8119842" "SRX8119849" "SRX8119850"
## ..$ SRS_accession: chr [1:4] "SRS6484446" "SRS6484447" "SRS6484454" "SRS6484455"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477856" "GSM4477857" "GSM4477864" "GSM4477865"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ 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" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119841" "SRX8119842" "SRX8119849" "SRX8119850"
## ..$ SRS_accession : chr [1:4] "SRS6484446" "SRS6484447" "SRS6484454" "SRS6484455"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477856" "GSM4477857" "GSM4477864" "GSM4477865"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477856" "GSM4477857" "GSM4477864" "GSM4477865"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01"
## ..$ LoadDate : chr [1:4] "2020-04-15 13:58:04" "2020-04-15 13:58:45" "2020-04-15 14:02:10" "2020-04-15 14:01:13"
## ..$ spots : int [1:4] 17221838 18368896 30026724 20607361
## ..$ bases : num [1:4] 1.31e+09 1.40e+09 2.28e+09 1.57e+09
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 445 475 777 532
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra57/SRR/011279/SRR11549939" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011279/SRR11549940" "https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/011279/SRR11549947" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/011279/SRR11549948"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484446" "SRS6484447" "SRS6484454" "SRS6484455"
## ..$ BioSample : chr [1:4] "SAMN14602090" "SAMN14602089" "SAMN14602130" "SAMN14602129"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "91A4AF4191B937E22ADFB29F41981109" "8B14206804D7B7027400A2E99825C386" "0ABB439E451B1577E1F6C5A4DA42CB98" "54DE7133EDCDE497777BDD261351DDE9"
## ..$ ReadHash : chr [1:4] "CF171BA7823579CC44DDF802D99D13C8" "96B1C0D2CCB8FDCECFFB8B659737DDD4" "55CC4609A91D16FE7EF921A80482DC68" "D2B71614F52026B2359979595B6A7D74"
## $ 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
## SRP256479: H1299 cells mock treatment versus infected with SARS-CoV-2 4 hours post infection: mock;SRX8119841,SRX8119842: SARS-CoV-2;SRX8119857,SRX8119858;## 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:
## ..$ SRR11549939: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549955: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549956: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549939: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549955: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549956: 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:
## ..$ SRR11549939: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549940: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549955: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549956: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119841" "SRX8119842" "SRX8119857" "SRX8119858"
## ..$ SRS_accession: chr [1:4] "SRS6484446" "SRS6484447" "SRS6484462" "SRS6484463"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477856" "GSM4477857" "GSM4477872" "GSM4477873"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ 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" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119841" "SRX8119842" "SRX8119857" "SRX8119858"
## ..$ SRS_accession : chr [1:4] "SRS6484446" "SRS6484447" "SRS6484462" "SRS6484463"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477856" "GSM4477857" "GSM4477872" "GSM4477873"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477856" "GSM4477857" "GSM4477872" "GSM4477873"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:02" "2020-05-05 09:32:02"
## ..$ LoadDate : chr [1:4] "2020-04-15 13:58:04" "2020-04-15 13:58:45" "2020-04-15 14:04:55" "2020-04-15 14:02:45"
## ..$ spots : int [1:4] 17221838 18368896 24805251 16393718
## ..$ bases : int [1:4] 1308859688 1396036096 1885199076 1245922568
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 445 475 641 424
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra57/SRR/011279/SRR11549939" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011279/SRR11549940" "https://sra-download.ncbi.nlm.nih.gov/traces/sra5/SRR/011279/SRR11549955" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011279/SRR11549956"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484446" "SRS6484447" "SRS6484462" "SRS6484463"
## ..$ BioSample : chr [1:4] "SAMN14602090" "SAMN14602089" "SAMN14602122" "SAMN14602121"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "91A4AF4191B937E22ADFB29F41981109" "8B14206804D7B7027400A2E99825C386" "A16FF697AA777133CEC25AFBE7688D56" "29E5FB73DA7A28CE8443CF9188EDCD66"
## ..$ ReadHash : chr [1:4] "CF171BA7823579CC44DDF802D99D13C8" "96B1C0D2CCB8FDCECFFB8B659737DDD4" "304EBFE1823D6B63B8ED5D8FC5744944" "83475421DA83198BE0198638B53F0B6C"
## $ 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
## SRP256479: H1299 cells mock treatment (36 and 4 hrs) versus infected with SARS-CoV-1 12 hours post infection:mock;SRX8119839,SRX8119840,SRX8119841,SRX8119842: SARS-CoV-1;SRX8119843,SRX8119844;## 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:
## ..$ SRR11549937: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549939: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549941: int [1:58302] 0 0 5 0 0 0 0 0 0 0 ...
## ..$ SRR11549942: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549937: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549939: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549941: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549942: 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:
## ..$ SRR11549937: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549938: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549939: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549940: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549941: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549942: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119839" "SRX8119840" "SRX8119841" "SRX8119842" ...
## ..$ SRS_accession: chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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] "SRX8119839" "SRX8119840" "SRX8119841" "SRX8119842" ...
## ..$ SRS_accession : chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 13:55:51" "2020-04-15 13:58:03" "2020-04-15 13:58:04" "2020-04-15 13:58:45" ...
## ..$ spots : int [1:6] 13925507 18362063 17221838 18368896 28777309 12894150
## ..$ bases : num [1:6] 1.06e+09 1.40e+09 1.31e+09 1.40e+09 2.19e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 372 473 445 475 742 336
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011279/SRR11549937" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011279/SRR11549938" "https://sra-download.ncbi.nlm.nih.gov/traces/sra57/SRR/011279/SRR11549939" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011279/SRR11549940" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ BioSample : chr [1:6] "SAMN14602092" "SAMN14602091" "SAMN14602090" "SAMN14602089" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "7EE11172BCBEEA2FA9B8C1E9FF2FB9ED" "6755414BE495BC3895B5A8FB4D7B25C7" "91A4AF4191B937E22ADFB29F41981109" "8B14206804D7B7027400A2E99825C386" ...
## ..$ ReadHash : chr [1:6] "0F923CF827EB5EE79B4A2CB570D33771" "A44DEF049D06B80DBC4358EC788258E8" "CF171BA7823579CC44DDF802D99D13C8" "96B1C0D2CCB8FDCECFFB8B659737DDD4" ...
## $ 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
## SRP256479: H1299 cells mock treatment (36 and 4 hrs) versus infected with SARS-CoV-1 24 hours post infection:mock;SRX8119839,SRX8119840,SRX8119841,SRX8119842: SARS-CoV-1;SRX8119845,SRX8119846;## 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:
## ..$ SRR11549937: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549939: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549943: int [1:58302] 0 0 2 0 0 0 0 0 0 1 ...
## ..$ SRR11549944: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549937: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549939: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549943: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549944: 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:
## ..$ SRR11549937: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549938: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549939: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549940: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549943: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549944: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119839" "SRX8119840" "SRX8119841" "SRX8119842" ...
## ..$ SRS_accession: chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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] "SRX8119839" "SRX8119840" "SRX8119841" "SRX8119842" ...
## ..$ SRS_accession : chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 13:55:51" "2020-04-15 13:58:03" "2020-04-15 13:58:04" "2020-04-15 13:58:45" ...
## ..$ spots : int [1:6] 13925507 18362063 17221838 18368896 18977804 21943958
## ..$ bases : int [1:6] 1058338532 1395516788 1308859688 1396036096 1442313104 1667740808
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 372 473 445 475 492 571
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011279/SRR11549937" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011279/SRR11549938" "https://sra-download.ncbi.nlm.nih.gov/traces/sra57/SRR/011279/SRR11549939" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011279/SRR11549940" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ BioSample : chr [1:6] "SAMN14602092" "SAMN14602091" "SAMN14602090" "SAMN14602089" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "7EE11172BCBEEA2FA9B8C1E9FF2FB9ED" "6755414BE495BC3895B5A8FB4D7B25C7" "91A4AF4191B937E22ADFB29F41981109" "8B14206804D7B7027400A2E99825C386" ...
## ..$ ReadHash : chr [1:6] "0F923CF827EB5EE79B4A2CB570D33771" "A44DEF049D06B80DBC4358EC788258E8" "CF171BA7823579CC44DDF802D99D13C8" "96B1C0D2CCB8FDCECFFB8B659737DDD4" ...
## $ 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
## SRP256479: H1299 cells mock treatment (36 and 4 hrs) versus infected with SARS-CoV-2 12 hours post infection:mock;SRX8119839,SRX8119840,SRX8119841,SRX8119842: SARS-CoV-2;SRX8119851,SRX8119852;## 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:
## ..$ SRR11549937: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549939: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549949: int [1:58302] 0 0 3 0 0 0 0 0 0 0 ...
## ..$ SRR11549950: int [1:58302] 0 1 3 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549937: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549939: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549949: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549950: 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:
## ..$ SRR11549937: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549938: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549939: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549940: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549949: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549950: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119839" "SRX8119840" "SRX8119841" "SRX8119842" ...
## ..$ SRS_accession: chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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] "SRX8119839" "SRX8119840" "SRX8119841" "SRX8119842" ...
## ..$ SRS_accession : chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 13:55:51" "2020-04-15 13:58:03" "2020-04-15 13:58:04" "2020-04-15 13:58:45" ...
## ..$ spots : int [1:6] 13925507 18362063 17221838 18368896 27517940 25747661
## ..$ bases : int [1:6] 1058338532 1395516788 1308859688 1396036096 2091363440 1956822236
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 372 473 445 475 710 664
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011279/SRR11549937" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011279/SRR11549938" "https://sra-download.ncbi.nlm.nih.gov/traces/sra57/SRR/011279/SRR11549939" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011279/SRR11549940" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ BioSample : chr [1:6] "SAMN14602092" "SAMN14602091" "SAMN14602090" "SAMN14602089" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "7EE11172BCBEEA2FA9B8C1E9FF2FB9ED" "6755414BE495BC3895B5A8FB4D7B25C7" "91A4AF4191B937E22ADFB29F41981109" "8B14206804D7B7027400A2E99825C386" ...
## ..$ ReadHash : chr [1:6] "0F923CF827EB5EE79B4A2CB570D33771" "A44DEF049D06B80DBC4358EC788258E8" "CF171BA7823579CC44DDF802D99D13C8" "96B1C0D2CCB8FDCECFFB8B659737DDD4" ...
## $ 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
## SRP256479: H1299 cells mock treatment (36 and 4 hrs) versus infected with SARS-CoV-2 24 hours post infection:mock;SRX8119839,SRX8119840,SRX8119841,SRX8119842: SARS-CoV-2;SRX8119853,SRX8119854;## 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:
## ..$ SRR11549937: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549939: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549951: int [1:58302] 0 0 5 0 0 0 0 0 0 0 ...
## ..$ SRR11549952: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549937: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549939: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549951: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549952: 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:
## ..$ SRR11549937: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549938: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549939: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549940: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549951: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549952: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119839" "SRX8119840" "SRX8119841" "SRX8119842" ...
## ..$ SRS_accession: chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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] "SRX8119839" "SRX8119840" "SRX8119841" "SRX8119842" ...
## ..$ SRS_accession : chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 13:55:51" "2020-04-15 13:58:03" "2020-04-15 13:58:04" "2020-04-15 13:58:45" ...
## ..$ spots : int [1:6] 13925507 18362063 17221838 18368896 28331222 26978550
## ..$ bases : num [1:6] 1.06e+09 1.40e+09 1.31e+09 1.40e+09 2.15e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 372 473 445 475 730 696
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011279/SRR11549937" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011279/SRR11549938" "https://sra-download.ncbi.nlm.nih.gov/traces/sra57/SRR/011279/SRR11549939" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011279/SRR11549940" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ BioSample : chr [1:6] "SAMN14602092" "SAMN14602091" "SAMN14602090" "SAMN14602089" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "7EE11172BCBEEA2FA9B8C1E9FF2FB9ED" "6755414BE495BC3895B5A8FB4D7B25C7" "91A4AF4191B937E22ADFB29F41981109" "8B14206804D7B7027400A2E99825C386" ...
## ..$ ReadHash : chr [1:6] "0F923CF827EB5EE79B4A2CB570D33771" "A44DEF049D06B80DBC4358EC788258E8" "CF171BA7823579CC44DDF802D99D13C8" "96B1C0D2CCB8FDCECFFB8B659737DDD4" ...
## $ 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
## SRP256479: H1299 cells mock treatment (36 and 4 hrs) versus untreated (4 hours) :mock;SRX8119839,SRX8119840,SRX8119841,SRX8119842: untreated;SRX8119859,SRX8119860;## 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:
## ..$ SRR11549937: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549939: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549957: int [1:58302] 0 3 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549958: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549937: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549938: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549939: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549940: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549957: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549958: 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:
## ..$ SRR11549937: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549938: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549939: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549940: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549957: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549958: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119839" "SRX8119840" "SRX8119841" "SRX8119842" ...
## ..$ SRS_accession: chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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] "SRX8119839" "SRX8119840" "SRX8119841" "SRX8119842" ...
## ..$ SRS_accession : chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477854" "GSM4477855" "GSM4477856" "GSM4477857" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" "2020-05-05 09:32:01" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 13:55:51" "2020-04-15 13:58:03" "2020-04-15 13:58:04" "2020-04-15 13:58:45" ...
## ..$ spots : int [1:6] 13925507 18362063 17221838 18368896 24914429 20748160
## ..$ bases : int [1:6] 1058338532 1395516788 1308859688 1396036096 1893496604 1576860160
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 372 473 445 475 645 533
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011279/SRR11549937" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011279/SRR11549938" "https://sra-download.ncbi.nlm.nih.gov/traces/sra57/SRR/011279/SRR11549939" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011279/SRR11549940" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484444" "SRS6484445" "SRS6484446" "SRS6484447" ...
## ..$ BioSample : chr [1:6] "SAMN14602092" "SAMN14602091" "SAMN14602090" "SAMN14602089" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "7EE11172BCBEEA2FA9B8C1E9FF2FB9ED" "6755414BE495BC3895B5A8FB4D7B25C7" "91A4AF4191B937E22ADFB29F41981109" "8B14206804D7B7027400A2E99825C386" ...
## ..$ ReadHash : chr [1:6] "0F923CF827EB5EE79B4A2CB570D33771" "A44DEF049D06B80DBC4358EC788258E8" "CF171BA7823579CC44DDF802D99D13C8" "96B1C0D2CCB8FDCECFFB8B659737DDD4" ...
## $ 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
## SRP256479: Caco2 cells mock treatment versus infected with SARS-CoV-1 24 hours post infection: mock;SRX8119861,SRX8119862: SARS-CoV-1;SRX8119867,SRX8119868;## 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:
## ..$ SRR11549959: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549960: int [1:58302] 0 3 3 0 0 0 0 0 0 0 ...
## ..$ SRR11549965: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549966: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549959: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549960: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549965: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549966: 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:
## ..$ SRR11549959: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549960: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549965: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549966: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "WARN(1,3,4,5,6,7)" "WARN(1,3,4,5,6,7)"
## ..$ SRX_accession: chr [1:4] "SRX8119861" "SRX8119862" "SRX8119867" "SRX8119868"
## ..$ SRS_accession: chr [1:4] "SRS6484465" "SRS6484467" "SRS6484472" "SRS6484473"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477876" "GSM4477877" "GSM4477882" "GSM4477883"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "WARN(1,3,4,5,6,7)" "WARN(1,3,4,5,6,7)"
## ..$ SRX_accession : chr [1:4] "SRX8119861" "SRX8119862" "SRX8119867" "SRX8119868"
## ..$ SRS_accession : chr [1:4] "SRS6484465" "SRS6484467" "SRS6484472" "SRS6484473"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477876" "GSM4477877" "GSM4477882" "GSM4477883"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477876" "GSM4477877" "GSM4477882" "GSM4477883"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:32:02"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:06:32" "2020-04-15 14:05:55" "2020-04-15 14:02:08" "2020-04-15 14:04:11"
## ..$ spots : int [1:4] 24340657 23455453 5912915 10389802
## ..$ bases : int [1:4] 1849889932 1782614428 449381540 789624952
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 682 659 170 291
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/011279/SRR11549959" "https://sra-download.ncbi.nlm.nih.gov/traces/sra36/SRR/011279/SRR11549960" "https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/011279/SRR11549965" "https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/011279/SRR11549966"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484465" "SRS6484467" "SRS6484472" "SRS6484473"
## ..$ BioSample : chr [1:4] "SAMN14602118" "SAMN14602117" "SAMN14602112" "SAMN14602111"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "B49B5CAEBFFF044E27CB20195E2C6474" "6AB4D257433BD4720B051C9E47563BCF" "F81C5719739C6F95CC47EBAEB9771F2E" "CA6BABC336F649D921AFD9F74AB52AC4"
## ..$ ReadHash : chr [1:4] "42F33DFAF8AB6AFC70EADE1DA424D9F3" "21D16B680249735C332C66B1748E8C5B" "B4B5C5CC1791C03553AB92FCC7988509" "235CFB042A353495992FD663887EBEF7"
## $ 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
## SRP256479: Caco2 cells mock treatment versus infected with SARS-CoV-1 4 hours post infection: mock;SRX8119863,SRX8119864: SARS-CoV-1;SRX8119869,SRX8119870;## 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:
## ..$ SRR11549961: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549962: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549967: int [1:58302] 0 0 4 0 0 0 0 0 0 0 ...
## ..$ SRR11549968: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549961: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549962: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549967: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549968: 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:
## ..$ SRR11549961: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549962: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549967: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549968: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119863" "SRX8119864" "SRX8119869" "SRX8119870"
## ..$ SRS_accession: chr [1:4] "SRS6484468" "SRS6484469" "SRS6484474" "SRS6484475"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477878" "GSM4477879" "GSM4477884" "GSM4477885"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ 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" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119863" "SRX8119864" "SRX8119869" "SRX8119870"
## ..$ SRS_accession : chr [1:4] "SRS6484468" "SRS6484469" "SRS6484474" "SRS6484475"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477878" "GSM4477879" "GSM4477884" "GSM4477885"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477878" "GSM4477879" "GSM4477884" "GSM4477885"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:32:02"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:03:23" "2020-04-15 14:05:20" "2020-04-15 14:08:27" "2020-04-15 14:10:41"
## ..$ spots : int [1:4] 17217824 23888929 20884931 27148315
## ..$ bases : int [1:4] 1308554624 1815558604 1587254756 2063271940
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 498 671 586 762
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011279/SRR11549961" "https://sra-download.ncbi.nlm.nih.gov/traces/sra43/SRR/011279/SRR11549962" "https://sra-download.ncbi.nlm.nih.gov/traces/sra75/SRR/011279/SRR11549967" "https://sra-download.ncbi.nlm.nih.gov/traces/sra78/SRR/011279/SRR11549968"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484468" "SRS6484469" "SRS6484474" "SRS6484475"
## ..$ BioSample : chr [1:4] "SAMN14602116" "SAMN14602115" "SAMN14602077" "SAMN14602076"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "F9534D593A133A77DF095F64B290F18A" "339FEF33D3305705ACDB1C485AA55F80" "4807866E3E5AED50D088B042E7ADB45B" "475335E1083FEE8CE72EAC8138BA7C65"
## ..$ ReadHash : chr [1:4] "40B9392E5C751546603368F652859DC4" "095744D49BBACE741B97296ACB855CB9" "09734695B7486F011DD28D381ACC2F0E" "6C98724C607CB8E074E0C3FD7CD1D048"
## $ 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
## SRP256479: Caco2 cells mock treatment versus infected with SARS-CoV-2 24 hours post infection:mock;SRX8119861,SRX8119862: SARS-CoV-1;SRX8119727,SRX8119728;## 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:
## ..$ SRR11549959: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549960: int [1:58302] 0 3 3 0 0 0 0 0 0 0 ...
## ..$ SRR11549971: int [1:58302] 0 1 3 0 0 0 0 0 0 0 ...
## ..$ SRR11549972: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549959: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549960: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549971: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549972: 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:
## ..$ SRR11549959: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549960: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549971: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549972: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "WARN(3,4,5)" "WARN(3,4,5,7)"
## ..$ SRX_accession: chr [1:4] "SRX8119861" "SRX8119862" "SRX8119727" "SRX8119728"
## ..$ SRS_accession: chr [1:4] "SRS6484465" "SRS6484467" "SRS6484332" "SRS6484333"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477876" "GSM4477877" "GSM4477888" "GSM4477889"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "WARN(3,4,5)" "WARN(3,4,5,7)"
## ..$ SRX_accession : chr [1:4] "SRX8119861" "SRX8119862" "SRX8119727" "SRX8119728"
## ..$ SRS_accession : chr [1:4] "SRS6484465" "SRS6484467" "SRS6484332" "SRS6484333"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477876" "GSM4477877" "GSM4477888" "GSM4477889"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477876" "GSM4477877" "GSM4477888" "GSM4477889"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:31:59" "2020-05-05 09:31:59"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:06:32" "2020-04-15 14:05:55" "2020-04-15 14:06:59" "2020-04-15 14:05:49"
## ..$ spots : int [1:4] 24340657 23455453 17235108 13303060
## ..$ bases : int [1:4] 1849889932 1782614428 1309868208 1011032560
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 682 659 486 372
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/011279/SRR11549959" "https://sra-download.ncbi.nlm.nih.gov/traces/sra36/SRR/011279/SRR11549960" "https://sra-download.ncbi.nlm.nih.gov/traces/sra8/SRR/011279/SRR11549971" "https://sra-download.ncbi.nlm.nih.gov/traces/sra71/SRR/011279/SRR11549972"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484465" "SRS6484467" "SRS6484332" "SRS6484333"
## ..$ BioSample : chr [1:4] "SAMN14602118" "SAMN14602117" "SAMN14602073" "SAMN14602072"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "B49B5CAEBFFF044E27CB20195E2C6474" "6AB4D257433BD4720B051C9E47563BCF" "32B580DA5DE253E02A60590B975B5C99" "2B7ED767780E6A947A267B5405517F06"
## ..$ ReadHash : chr [1:4] "42F33DFAF8AB6AFC70EADE1DA424D9F3" "21D16B680249735C332C66B1748E8C5B" "5BCEC793D6EEC128E4F9F65B9B937FF2" "9D82D08D579F32DC44F5DB52552FF1C0"
## $ 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
## SRP256479: Caco2 cells mock treatment versus infected with SARS-CoV-2 4 hours post infection:mock;SRX8119863,SRX8119864: SARS-CoV-2;SRX8119729,SRX8119730;## 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:
## ..$ SRR11549961: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549962: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549973: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549974: int [1:58302] 1 2 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549961: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549962: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549973: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549974: 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:
## ..$ SRR11549961: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549962: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549973: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549974: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "WARN(1,5,7)" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119863" "SRX8119864" "SRX8119729" "SRX8119730"
## ..$ SRS_accession: chr [1:4] "SRS6484468" "SRS6484469" "SRS6484334" "SRS6484335"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477878" "GSM4477879" "GSM4477890" "GSM4477891"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "WARN(1,5,7)" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119863" "SRX8119864" "SRX8119729" "SRX8119730"
## ..$ SRS_accession : chr [1:4] "SRS6484468" "SRS6484469" "SRS6484334" "SRS6484335"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477878" "GSM4477879" "GSM4477890" "GSM4477891"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477878" "GSM4477879" "GSM4477890" "GSM4477891"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:31:59" "2020-05-05 09:31:59"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:03:23" "2020-04-15 14:05:20" "2020-04-15 14:05:12" "2020-04-15 14:06:39"
## ..$ spots : int [1:4] 17217824 23888929 8836339 13789240
## ..$ bases : int [1:4] 1308554624 1815558604 671561764 1047982240
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 498 671 250 389
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011279/SRR11549961" "https://sra-download.ncbi.nlm.nih.gov/traces/sra43/SRR/011279/SRR11549962" "https://sra-download.ncbi.nlm.nih.gov/traces/sra39/SRR/011279/SRR11549973" "https://sra-download.ncbi.nlm.nih.gov/traces/sra67/SRR/011279/SRR11549974"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484468" "SRS6484469" "SRS6484334" "SRS6484335"
## ..$ BioSample : chr [1:4] "SAMN14602116" "SAMN14602115" "SAMN14602071" "SAMN14602070"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "F9534D593A133A77DF095F64B290F18A" "339FEF33D3305705ACDB1C485AA55F80" "471F0793E91B972EA9018D5CC1CB2382" "7798F9624DAAB728320D715745597026"
## ..$ ReadHash : chr [1:4] "40B9392E5C751546603368F652859DC4" "095744D49BBACE741B97296ACB855CB9" "33D157E7954EFC69B5CC6CBAD82BE219" "169890A8C66FCF1C20473DE7F66634B9"
## $ 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
## SRP256479: Caco2 cells mock treatment (4 and 24 hrs) versus infected with SARS-CoV-1 12 hours post infection: mock;SRX8119861,SRX8119862,SRX8119863,SRX8119864: SARS-CoV-1;SRX8119865,SRX8119866;## 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:
## ..$ SRR11549959: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549960: int [1:58302] 0 3 3 0 0 0 0 0 0 0 ...
## ..$ SRR11549961: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549962: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549963: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549964: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549959: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549960: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549961: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549962: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549963: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549964: 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:
## ..$ SRR11549959: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549960: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549961: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549962: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549963: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549964: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119861" "SRX8119862" "SRX8119863" "SRX8119864" ...
## ..$ SRS_accession: chr [1:6] "SRS6484465" "SRS6484467" "SRS6484468" "SRS6484469" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477876" "GSM4477877" "GSM4477878" "GSM4477879" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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] "SRX8119861" "SRX8119862" "SRX8119863" "SRX8119864" ...
## ..$ SRS_accession : chr [1:6] "SRS6484465" "SRS6484467" "SRS6484468" "SRS6484469" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477876" "GSM4477877" "GSM4477878" "GSM4477879" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477876" "GSM4477877" "GSM4477878" "GSM4477879" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:32:02" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 14:06:32" "2020-04-15 14:05:55" "2020-04-15 14:03:23" "2020-04-15 14:05:20" ...
## ..$ spots : int [1:6] 24340657 23455453 17217824 23888929 16222543 11417164
## ..$ bases : int [1:6] 1849889932 1782614428 1308554624 1815558604 1232913268 867704464
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 682 659 498 671 453 320
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/011279/SRR11549959" "https://sra-download.ncbi.nlm.nih.gov/traces/sra36/SRR/011279/SRR11549960" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011279/SRR11549961" "https://sra-download.ncbi.nlm.nih.gov/traces/sra43/SRR/011279/SRR11549962" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484465" "SRS6484467" "SRS6484468" "SRS6484469" ...
## ..$ BioSample : chr [1:6] "SAMN14602118" "SAMN14602117" "SAMN14602116" "SAMN14602115" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "B49B5CAEBFFF044E27CB20195E2C6474" "6AB4D257433BD4720B051C9E47563BCF" "F9534D593A133A77DF095F64B290F18A" "339FEF33D3305705ACDB1C485AA55F80" ...
## ..$ ReadHash : chr [1:6] "42F33DFAF8AB6AFC70EADE1DA424D9F3" "21D16B680249735C332C66B1748E8C5B" "40B9392E5C751546603368F652859DC4" "095744D49BBACE741B97296ACB855CB9" ...
## $ 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
## SRP256479: Caco2 cells mock treatment (4 and 24 hrs) versus untreated (4 hours): mock;SRX8119861,SRX8119862,SRX8119863,SRX8119864: untreated;SRX8119731,SRX8119732;## 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:
## ..$ SRR11549959: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549960: int [1:58302] 0 3 3 0 0 0 0 0 0 0 ...
## ..$ SRR11549961: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549962: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549975: int [1:58302] 0 1 3 0 0 0 0 0 0 0 ...
## ..$ SRR11549976: int [1:58302] 0 3 4 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549959: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549960: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549961: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549962: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549975: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549976: 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:
## ..$ SRR11549959: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549960: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549961: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549962: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549975: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549976: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119861" "SRX8119862" "SRX8119863" "SRX8119864" ...
## ..$ SRS_accession: chr [1:6] "SRS6484465" "SRS6484467" "SRS6484468" "SRS6484469" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477876" "GSM4477877" "GSM4477878" "GSM4477879" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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] "SRX8119861" "SRX8119862" "SRX8119863" "SRX8119864" ...
## ..$ SRS_accession : chr [1:6] "SRS6484465" "SRS6484467" "SRS6484468" "SRS6484469" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477876" "GSM4477877" "GSM4477878" "GSM4477879" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477876" "GSM4477877" "GSM4477878" "GSM4477879" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:32:02" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 14:06:32" "2020-04-15 14:05:55" "2020-04-15 14:03:23" "2020-04-15 14:05:20" ...
## ..$ spots : int [1:6] 24340657 23455453 17217824 23888929 21858655 23219094
## ..$ bases : int [1:6] 1849889932 1782614428 1308554624 1815558604 1661257780 1764651144
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 682 659 498 671 614 652
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/011279/SRR11549959" "https://sra-download.ncbi.nlm.nih.gov/traces/sra36/SRR/011279/SRR11549960" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011279/SRR11549961" "https://sra-download.ncbi.nlm.nih.gov/traces/sra43/SRR/011279/SRR11549962" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484465" "SRS6484467" "SRS6484468" "SRS6484469" ...
## ..$ BioSample : chr [1:6] "SAMN14602118" "SAMN14602117" "SAMN14602116" "SAMN14602115" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "B49B5CAEBFFF044E27CB20195E2C6474" "6AB4D257433BD4720B051C9E47563BCF" "F9534D593A133A77DF095F64B290F18A" "339FEF33D3305705ACDB1C485AA55F80" ...
## ..$ ReadHash : chr [1:6] "42F33DFAF8AB6AFC70EADE1DA424D9F3" "21D16B680249735C332C66B1748E8C5B" "40B9392E5C751546603368F652859DC4" "095744D49BBACE741B97296ACB855CB9" ...
## $ 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
## SRP256479: Caco2 cells mock treatment (4 and 24 hrs) versus infected with SARS-CoV-2 12 hours post infection: mock;SRX8119861,SRX8119862,SRX8119863,SRX8119864: SARS-CoV-2;SRX8119871,SRX8119872;## 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:
## ..$ SRR11549959: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549960: int [1:58302] 0 3 3 0 0 0 0 0 0 0 ...
## ..$ SRR11549961: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549962: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549969: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR11549970: int [1:58302] 1 0 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549959: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549960: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549961: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549962: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549969: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549970: 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:
## ..$ SRR11549959: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549960: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549961: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549962: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549969: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549970: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119861" "SRX8119862" "SRX8119863" "SRX8119864" ...
## ..$ SRS_accession: chr [1:6] "SRS6484465" "SRS6484467" "SRS6484468" "SRS6484469" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477876" "GSM4477877" "GSM4477878" "GSM4477879" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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] "SRX8119861" "SRX8119862" "SRX8119863" "SRX8119864" ...
## ..$ SRS_accession : chr [1:6] "SRS6484465" "SRS6484467" "SRS6484468" "SRS6484469" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477876" "GSM4477877" "GSM4477878" "GSM4477879" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477876" "GSM4477877" "GSM4477878" "GSM4477879" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:32:02" "2020-05-05 09:32:02" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 14:06:32" "2020-04-15 14:05:55" "2020-04-15 14:03:23" "2020-04-15 14:05:20" ...
## ..$ spots : int [1:6] 24340657 23455453 17217824 23888929 21261335 18094474
## ..$ bases : int [1:6] 1849889932 1782614428 1308554624 1815558604 1615861460 1375180024
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 682 659 498 671 594 511
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/011279/SRR11549959" "https://sra-download.ncbi.nlm.nih.gov/traces/sra36/SRR/011279/SRR11549960" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011279/SRR11549961" "https://sra-download.ncbi.nlm.nih.gov/traces/sra43/SRR/011279/SRR11549962" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484465" "SRS6484467" "SRS6484468" "SRS6484469" ...
## ..$ BioSample : chr [1:6] "SAMN14602118" "SAMN14602117" "SAMN14602116" "SAMN14602115" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "B49B5CAEBFFF044E27CB20195E2C6474" "6AB4D257433BD4720B051C9E47563BCF" "F9534D593A133A77DF095F64B290F18A" "339FEF33D3305705ACDB1C485AA55F80" ...
## ..$ ReadHash : chr [1:6] "42F33DFAF8AB6AFC70EADE1DA424D9F3" "21D16B680249735C332C66B1748E8C5B" "40B9392E5C751546603368F652859DC4" "095744D49BBACE741B97296ACB855CB9" ...
## $ 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
## SRP256479: Series 1 Calu3 cells mock treatment versus untreated (4 hours): mock;SRX8119735,SRX8119736: untreated;SRX8119733,SRX8119734;## 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:
## ..$ SRR11549977: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR11549978: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR11549979: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR11549980: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549977: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549978: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549980: 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:
## ..$ SRR11549977: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549978: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549979: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549980: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(5,7)" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119733" "SRX8119734" "SRX8119735" "SRX8119736"
## ..$ SRS_accession: chr [1:4] "SRS6484338" "SRS6484339" "SRS6484340" "SRS6484341"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477894" "GSM4477895" "GSM4477896" "GSM4477897"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "WARN(1,5,7)" "WARN(1,5,7)" "WARN(5,7)" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119733" "SRX8119734" "SRX8119735" "SRX8119736"
## ..$ SRS_accession : chr [1:4] "SRS6484338" "SRS6484339" "SRS6484340" "SRS6484341"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477894" "GSM4477895" "GSM4477896" "GSM4477897"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477894" "GSM4477895" "GSM4477896" "GSM4477897"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:31:59"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:06:58" "2020-04-15 14:07:03" "2020-04-15 14:07:34" "2020-04-15 14:09:28"
## ..$ spots : int [1:4] 9281817 9700015 11708898 13746112
## ..$ bases : int [1:4] 705418092 737201140 889876248 1044704512
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 263 273 330 385
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra35/SRR/011279/SRR11549977" "https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/011279/SRR11549978" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011279/SRR11549979" "https://sra-download.ncbi.nlm.nih.gov/traces/sra5/SRR/011279/SRR11549980"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484338" "SRS6484339" "SRS6484340" "SRS6484341"
## ..$ BioSample : chr [1:4] "SAMN14602067" "SAMN14602066" "SAMN14602065" "SAMN14602064"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "10EBAA4E6F07B27F920DFAB5AD2EE760" "78383D68122141DB6A7A92CE673A57F6" "2985EEEDB8B0433B8BF26CB5E98C879F" "658A6443CD156AC76584AD5BCBA62ED8"
## ..$ ReadHash : chr [1:4] "7274E04E202ADE3C1FDFEF491AE063A3" "BF602DD30225609BD44964ADEF81B093" "F187ABE78C381D1811C7AAB93D229790" "463113C301319EDFF9C46DD8DD91BBE3"
## $ 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
## SRP256479: Series 1 Calu3 cells mock treatment versus infected with SARS-CoV-1 4 hours post infection: mock;SRX8119735,SRX8119736: SARS-CoV-1;SRX8119739,SRX8119740;## 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:
## ..$ SRR11549979: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR11549980: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549983: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549984: int [1:58302] 0 3 1 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549983: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549984: 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:
## ..$ SRR11549979: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549980: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549983: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549984: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "WARN(5,7)" "PASS" "WARN(5,7)" "WARN(5,7)"
## ..$ SRX_accession: chr [1:4] "SRX8119735" "SRX8119736" "SRX8119739" "SRX8119740"
## ..$ SRS_accession: chr [1:4] "SRS6484340" "SRS6484341" "SRS6484344" "SRS6484345"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477896" "GSM4477897" "GSM4477900" "GSM4477901"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "WARN(5,7)" "PASS" "WARN(5,7)" "WARN(5,7)"
## ..$ SRX_accession : chr [1:4] "SRX8119735" "SRX8119736" "SRX8119739" "SRX8119740"
## ..$ SRS_accession : chr [1:4] "SRS6484340" "SRS6484341" "SRS6484344" "SRS6484345"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477896" "GSM4477897" "GSM4477900" "GSM4477901"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477896" "GSM4477897" "GSM4477900" "GSM4477901"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:31:59"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:07:34" "2020-04-15 14:09:28" "2020-04-15 14:08:01" "2020-04-15 14:08:54"
## ..$ spots : int [1:4] 11708898 13746112 10784532 11165637
## ..$ bases : int [1:4] 889876248 1044704512 819624432 848588412
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 330 385 305 319
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011279/SRR11549979" "https://sra-download.ncbi.nlm.nih.gov/traces/sra5/SRR/011279/SRR11549980" "https://sra-download.ncbi.nlm.nih.gov/traces/sra41/SRR/011279/SRR11549983" "https://sra-download.ncbi.nlm.nih.gov/traces/sra57/SRR/011279/SRR11549984"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484340" "SRS6484341" "SRS6484344" "SRS6484345"
## ..$ BioSample : chr [1:4] "SAMN14602065" "SAMN14602064" "SAMN14602106" "SAMN14602105"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "2985EEEDB8B0433B8BF26CB5E98C879F" "658A6443CD156AC76584AD5BCBA62ED8" "7A5506A26BCBBF1570CAAF9C7E78EFAD" "755A8B42C0BA3E8E5B686146A7021725"
## ..$ ReadHash : chr [1:4] "F187ABE78C381D1811C7AAB93D229790" "463113C301319EDFF9C46DD8DD91BBE3" "CDB7B935367F3539C54F575CE0EEC404" "1C929BE5A507854799FDCEF9CB3662FE"
## $ 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
## SRP256479: Series 1 Calu3 cells mock treatment versus infected with SARS-CoV-1 24 hours post infection: mock;SRX8119737, SRX8119738: SARS-CoV-1;SRX8119743,SRX8119744;## 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:
## ..$ SRR11549981: int [1:58302] 0 3 1 0 0 0 0 0 0 3 ...
## ..$ SRR11549987: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549988: int [1:58302] 0 3 1 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 3 variables:
## ..$ SRR11549981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549987: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549988: 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:
## ..$ SRR11549981: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549987: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549988: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 3 obs. of 7 variables:
## ..$ QC_summary : chr [1:3] "PASS" "FAIL(3)" "FAIL(3)"
## ..$ SRX_accession: chr [1:3] "SRX8119737" "SRX8119743" "SRX8119744"
## ..$ SRS_accession: chr [1:3] "SRS6484342" "SRS6484348" "SRS6484349"
## ..$ SRP_accession: chr [1:3] "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:3] "GSM4477898" "GSM4477904" "GSM4477905"
## ..$ GEO_series : chr [1:3] "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:3] NA NA NA
## $ MetadataFull :'data.frame': 3 obs. of 52 variables:
## ..$ QC_summary : chr [1:3] "PASS" "FAIL(3)" "FAIL(3)"
## ..$ SRX_accession : chr [1:3] "SRX8119737" "SRX8119743" "SRX8119744"
## ..$ SRS_accession : chr [1:3] "SRS6484342" "SRS6484348" "SRS6484349"
## ..$ SRP_accession : chr [1:3] "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:3] "GSM4477898" "GSM4477904" "GSM4477905"
## ..$ GEO_series : chr [1:3] "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:3] NA NA NA
## ..$ SampleName : chr [1:3] "GSM4477898" "GSM4477904" "GSM4477905"
## ..$ ReleaseDate : chr [1:3] "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:31:59"
## ..$ LoadDate : chr [1:3] "2020-04-15 14:10:59" "2020-04-15 14:12:24" "2020-04-15 14:11:04"
## ..$ spots : int [1:3] 19572498 14436863 17023394
## ..$ bases : int [1:3] 1487509848 1097201588 1293777944
## ..$ spots_with_mates : int [1:3] 0 0 0
## ..$ avgLength : int [1:3] 76 76 76
## ..$ size_MB : int [1:3] 548 404 475
## ..$ AssemblyName : logi [1:3] NA NA NA
## ..$ download_path : chr [1:3] "https://sra-download.ncbi.nlm.nih.gov/traces/sra73/SRR/011279/SRR11549981" "https://sra-download.ncbi.nlm.nih.gov/traces/sra74/SRR/011279/SRR11549987" "https://sra-download.ncbi.nlm.nih.gov/traces/sra78/SRR/011279/SRR11549988"
## ..$ 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] "SINGLE" "SINGLE" "SINGLE"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:3] "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:3] "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:3] NA NA NA
## ..$ ProjectID : int [1:3] 625518 625518 625518
## ..$ Sample : chr [1:3] "SRS6484342" "SRS6484348" "SRS6484349"
## ..$ BioSample : chr [1:3] "SAMN14602108" "SAMN14602102" "SAMN14602101"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:3] NA NA NA
## ..$ Consent : chr [1:3] "public" "public" "public"
## ..$ RunHash : chr [1:3] "5B63E4B0288611918B6BBBADD102F614" "A3696F36C05D4F6901287922B436C1D1" "AA7B5E3F3F0D92D41A9C3AF1D8FEEC06"
## ..$ ReadHash : chr [1:3] "91A7550DC344405F20EEECA4E66842BF" "FB54C047BEA3AABCB708A41B84AEDDF8" "1846CE1DFA2A2E0D21FA4A1E7F523E10"
## $ absent : chr(0)## SRP256479: Series 1 Calu3 cells mock treatment (4 and 24 hrs) versus infected with SARS-CoV-1 12 hours post infection: mock;SRX8119735,SRX8119736,SRX8119737,SRX8119738: SARS-CoV-1;SRX8119741,SRX8119742;
## 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:
## ..$ SRR11549979: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR11549980: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549981: int [1:58302] 0 3 1 0 0 0 0 0 0 3 ...
## ..$ SRR11549982: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549985: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549986: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549982: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549985: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549986: 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:
## ..$ SRR11549979: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549980: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549981: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549982: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549985: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549986: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(5,7)" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119735" "SRX8119736" "SRX8119737" "SRX8119738" ...
## ..$ SRS_accession: chr [1:6] "SRS6484340" "SRS6484341" "SRS6484342" "SRS6484343" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477896" "GSM4477897" "GSM4477898" "GSM4477899" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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(5,7)" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX8119735" "SRX8119736" "SRX8119737" "SRX8119738" ...
## ..$ SRS_accession : chr [1:6] "SRS6484340" "SRS6484341" "SRS6484342" "SRS6484343" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477896" "GSM4477897" "GSM4477898" "GSM4477899" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477896" "GSM4477897" "GSM4477898" "GSM4477899" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:31:59" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 14:07:34" "2020-04-15 14:09:28" "2020-04-15 14:10:59" "2020-04-15 14:12:38" ...
## ..$ spots : int [1:6] 11708898 13746112 19572498 23845184 11437618 9061927
## ..$ bases : int [1:6] 889876248 1044704512 1487509848 1812233984 869258968 688706452
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 330 385 548 668 321 256
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011279/SRR11549979" "https://sra-download.ncbi.nlm.nih.gov/traces/sra5/SRR/011279/SRR11549980" "https://sra-download.ncbi.nlm.nih.gov/traces/sra73/SRR/011279/SRR11549981" "https://sra-download.ncbi.nlm.nih.gov/traces/sra75/SRR/011279/SRR11549982" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484340" "SRS6484341" "SRS6484342" "SRS6484343" ...
## ..$ BioSample : chr [1:6] "SAMN14602065" "SAMN14602064" "SAMN14602108" "SAMN14602107" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "2985EEEDB8B0433B8BF26CB5E98C879F" "658A6443CD156AC76584AD5BCBA62ED8" "5B63E4B0288611918B6BBBADD102F614" "7A098ACFAD83DD08811D4DE34BCC1497" ...
## ..$ ReadHash : chr [1:6] "F187ABE78C381D1811C7AAB93D229790" "463113C301319EDFF9C46DD8DD91BBE3" "91A7550DC344405F20EEECA4E66842BF" "6BE2DF4181C38D5E82EC5981C7C7EEFB" ...
## $ 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
## SRP256479: Series 1 Calu3 cells mock treatment versus infected with SARS-CoV-2 4 hours post infection: mock;SRX8119735,SRX8119736: SARS-CoV-2;SRX8119745,SRX8119746;## 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:
## ..$ SRR11549979: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR11549980: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549989: int [1:58302] 0 1 1 0 0 0 0 0 0 2 ...
## ..$ SRR11549990: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549989: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549990: 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:
## ..$ SRR11549979: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549980: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549989: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549990: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "WARN(5,7)" "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119735" "SRX8119736" "SRX8119745" "SRX8119746"
## ..$ SRS_accession: chr [1:4] "SRS6484340" "SRS6484341" "SRS6484350" "SRS6484351"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477896" "GSM4477897" "GSM4477906" "GSM4477907"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "WARN(5,7)" "PASS" "PASS" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119735" "SRX8119736" "SRX8119745" "SRX8119746"
## ..$ SRS_accession : chr [1:4] "SRS6484340" "SRS6484341" "SRS6484350" "SRS6484351"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477896" "GSM4477897" "GSM4477906" "GSM4477907"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477896" "GSM4477897" "GSM4477906" "GSM4477907"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:07:34" "2020-04-15 14:09:28" "2020-04-15 14:11:35" "2020-04-15 14:12:04"
## ..$ spots : int [1:4] 11708898 13746112 14535594 17211547
## ..$ bases : int [1:4] 889876248 1044704512 1104705144 1308077572
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 330 385 409 483
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011279/SRR11549979" "https://sra-download.ncbi.nlm.nih.gov/traces/sra5/SRR/011279/SRR11549980" "https://sra-download.ncbi.nlm.nih.gov/traces/sra16/SRR/011279/SRR11549989" "https://sra-download.ncbi.nlm.nih.gov/traces/sra62/SRR/011279/SRR11549990"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484340" "SRS6484341" "SRS6484350" "SRS6484351"
## ..$ BioSample : chr [1:4] "SAMN14602065" "SAMN14602064" "SAMN14602100" "SAMN14602099"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "2985EEEDB8B0433B8BF26CB5E98C879F" "658A6443CD156AC76584AD5BCBA62ED8" "83CA1FF7C38A1031BC0D5367009FC2A2" "C04AFEC2D8A9842AA1047FD620228010"
## ..$ ReadHash : chr [1:4] "F187ABE78C381D1811C7AAB93D229790" "463113C301319EDFF9C46DD8DD91BBE3" "0FC3C3381983593BF6EC061549ADC811" "882FEBC7BBCE4FB88FDD29B20C803D10"
## $ 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
## SRP256479: Series 1 Calu3 cells mock treatment versus infected with SARS-CoV-2 24 hours post infection: mock;SRX8119737, SRX8119738: SARS-CoV-2;SRX8119749,SRX8119750;## 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:
## ..$ SRR11549981: int [1:58302] 0 3 1 0 0 0 0 0 0 3 ...
## ..$ SRR11549993: int [1:58302] 0 1 1 0 0 0 0 0 0 3 ...
## ..$ SRR11549994: int [1:58302] 0 0 1 0 0 0 0 0 0 2 ...
## $ TxCounts :'data.frame': 180869 obs. of 3 variables:
## ..$ SRR11549981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549993: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549994: 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:
## ..$ SRR11549981: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549993: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549994: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 3 obs. of 7 variables:
## ..$ QC_summary : chr [1:3] "PASS" "WARN(1,5,7)" "WARN(1,5,7)"
## ..$ SRX_accession: chr [1:3] "SRX8119737" "SRX8119749" "SRX8119750"
## ..$ SRS_accession: chr [1:3] "SRS6484342" "SRS6484354" "SRS6484355"
## ..$ SRP_accession: chr [1:3] "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:3] "GSM4477898" "GSM4477910" "GSM4477911"
## ..$ GEO_series : chr [1:3] "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:3] NA NA NA
## $ MetadataFull :'data.frame': 3 obs. of 52 variables:
## ..$ QC_summary : chr [1:3] "PASS" "WARN(1,5,7)" "WARN(1,5,7)"
## ..$ SRX_accession : chr [1:3] "SRX8119737" "SRX8119749" "SRX8119750"
## ..$ SRS_accession : chr [1:3] "SRS6484342" "SRS6484354" "SRS6484355"
## ..$ SRP_accession : chr [1:3] "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:3] "GSM4477898" "GSM4477910" "GSM4477911"
## ..$ GEO_series : chr [1:3] "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:3] NA NA NA
## ..$ SampleName : chr [1:3] "GSM4477898" "GSM4477910" "GSM4477911"
## ..$ ReleaseDate : chr [1:3] "2020-05-05 09:31:59" "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:3] "2020-04-15 14:10:59" "2020-04-15 14:09:23" "2020-04-15 14:10:39"
## ..$ spots : int [1:3] 19572498 7679519 9799418
## ..$ bases : int [1:3] 1487509848 583643444 744755768
## ..$ spots_with_mates : int [1:3] 0 0 0
## ..$ avgLength : int [1:3] 76 76 76
## ..$ size_MB : int [1:3] 548 217 276
## ..$ AssemblyName : logi [1:3] NA NA NA
## ..$ download_path : chr [1:3] "https://sra-download.ncbi.nlm.nih.gov/traces/sra73/SRR/011279/SRR11549981" "https://sra-download.ncbi.nlm.nih.gov/traces/sra65/SRR/011279/SRR11549993" "https://sra-download.ncbi.nlm.nih.gov/traces/sra34/SRR/011279/SRR11549994"
## ..$ 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] "SINGLE" "SINGLE" "SINGLE"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:3] "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:3] "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:3] NA NA NA
## ..$ ProjectID : int [1:3] 625518 625518 625518
## ..$ Sample : chr [1:3] "SRS6484342" "SRS6484354" "SRS6484355"
## ..$ BioSample : chr [1:3] "SAMN14602108" "SAMN14602096" "SAMN14602095"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:3] NA NA NA
## ..$ Consent : chr [1:3] "public" "public" "public"
## ..$ RunHash : chr [1:3] "5B63E4B0288611918B6BBBADD102F614" "2323FF6A8F2F49C56C8B27CE8192F580" "92E126AFAD7DE013B4F436606DB953A6"
## ..$ ReadHash : chr [1:3] "91A7550DC344405F20EEECA4E66842BF" "45CF2393E532D7D1D5DF9E8750E8A6F6" "5F1734470EB6B6536F371B85F8977BB0"
## $ absent : chr(0)## SRP256479: Series 1 Calu3 cells mock treatment (4 and 24 hrs) versus infected with SARS-CoV-2 12 hours post infection: mock;SRX8119735,SRX8119736,SRX8119737,SRX8119738: SARS-CoV-2;SRX8119747,SRX8119748;
## 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:
## ..$ SRR11549979: int [1:58302] 0 1 0 0 0 0 0 0 0 1 ...
## ..$ SRR11549980: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549981: int [1:58302] 0 3 1 0 0 0 0 0 0 3 ...
## ..$ SRR11549982: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR11549991: int [1:58302] 0 0 0 0 0 0 0 0 0 2 ...
## ..$ SRR11549992: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549982: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549991: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11549992: 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:
## ..$ SRR11549979: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549980: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549981: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549982: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549991: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11549992: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(5,7)" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119735" "SRX8119736" "SRX8119737" "SRX8119738" ...
## ..$ SRS_accession: chr [1:6] "SRS6484340" "SRS6484341" "SRS6484342" "SRS6484343" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477896" "GSM4477897" "GSM4477898" "GSM4477899" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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(5,7)" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX8119735" "SRX8119736" "SRX8119737" "SRX8119738" ...
## ..$ SRS_accession : chr [1:6] "SRS6484340" "SRS6484341" "SRS6484342" "SRS6484343" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477896" "GSM4477897" "GSM4477898" "GSM4477899" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477896" "GSM4477897" "GSM4477898" "GSM4477899" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:31:59" "2020-05-05 09:31:59" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 14:07:34" "2020-04-15 14:09:28" "2020-04-15 14:10:59" "2020-04-15 14:12:38" ...
## ..$ spots : int [1:6] 11708898 13746112 19572498 23845184 11433667 8260125
## ..$ bases : int [1:6] 889876248 1044704512 1487509848 1812233984 868958692 627769500
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 330 385 548 668 320 232
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011279/SRR11549979" "https://sra-download.ncbi.nlm.nih.gov/traces/sra5/SRR/011279/SRR11549980" "https://sra-download.ncbi.nlm.nih.gov/traces/sra73/SRR/011279/SRR11549981" "https://sra-download.ncbi.nlm.nih.gov/traces/sra75/SRR/011279/SRR11549982" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484340" "SRS6484341" "SRS6484342" "SRS6484343" ...
## ..$ BioSample : chr [1:6] "SAMN14602065" "SAMN14602064" "SAMN14602108" "SAMN14602107" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "2985EEEDB8B0433B8BF26CB5E98C879F" "658A6443CD156AC76584AD5BCBA62ED8" "5B63E4B0288611918B6BBBADD102F614" "7A098ACFAD83DD08811D4DE34BCC1497" ...
## ..$ ReadHash : chr [1:6] "F187ABE78C381D1811C7AAB93D229790" "463113C301319EDFF9C46DD8DD91BBE3" "91A7550DC344405F20EEECA4E66842BF" "6BE2DF4181C38D5E82EC5981C7C7EEFB" ...
## $ 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
## SRP256479: Series 2 Calu3 cells mock treatment versus infected with SARS-CoV-1 12 hours post infection: mock;SRX8119755,SRX8119756: SARS-CoV-1;SRX8119757,SRX8119758;## 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:
## ..$ SRR11549999: int [1:58302] 1 4 2 0 0 0 0 0 0 2 ...
## ..$ SRR11550000: int [1:58302] 0 1 3 0 0 0 0 0 0 0 ...
## ..$ SRR11550001: int [1:58302] 0 1 3 0 0 0 0 0 0 1 ...
## ..$ SRR11550002: int [1:58302] 0 3 1 0 0 0 0 0 0 3 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549999: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550000: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550001: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550002: 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:
## ..$ SRR11549999: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550000: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550001: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550002: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119755" "SRX8119756" "SRX8119757" "SRX8119758"
## ..$ SRS_accession: chr [1:4] "SRS6484360" "SRS6484361" "SRS6484362" "SRS6484363"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477916" "GSM4477917" "GSM4477918" "GSM4477919"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ 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" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119755" "SRX8119756" "SRX8119757" "SRX8119758"
## ..$ SRS_accession : chr [1:4] "SRS6484360" "SRS6484361" "SRS6484362" "SRS6484363"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477916" "GSM4477917" "GSM4477918" "GSM4477919"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477916" "GSM4477917" "GSM4477918" "GSM4477919"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:13:13" "2020-04-15 14:15:26" "2020-04-15 14:19:22" "2020-04-15 14:14:46"
## ..$ spots : int [1:4] 16689791 17520017 29798551 22962834
## ..$ bases : num [1:4] 1.27e+09 1.33e+09 2.26e+09 1.75e+09
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 465 478 802 617
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra75/SRR/011279/SRR11549999" "https://sra-download.ncbi.nlm.nih.gov/traces/sra74/SRR/011279/SRR11550000" "https://sra-download.ncbi.nlm.nih.gov/traces/sra70/SRR/011279/SRR11550001" "https://sra-download.ncbi.nlm.nih.gov/traces/sra78/SRR/011279/SRR11550002"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484360" "SRS6484361" "SRS6484362" "SRS6484363"
## ..$ BioSample : chr [1:4] "SAMN14602061" "SAMN14602060" "SAMN14602043" "SAMN14602042"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "650F29C7F837170003E35A519A4BCF97" "22D94DE04FFB9A3FCBC7532FED779E8D" "83F0AAFC8668B2223F61165F36FB4D87" "9549889C2FFCDF9D012A43CF18312301"
## ..$ ReadHash : chr [1:4] "19AB89BFCEA4679F97BC34DA2E341B5C" "049FF2155DADA5D9126E8D5222A52A17" "518B68E2D06C8FEAC503815FC4B26712" "2A09C7878343B958AB57CBA4B02CDF69"
## $ 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
## SRP256479: Series 2 Calu3 cells mock treatment versus infected with SARS-CoV-2 12 hours post infection: mock;SRX8119755,SRX8119756: SARS-CoV-2;SRX8119759,SRX8119760;## 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:
## ..$ SRR11549999: int [1:58302] 1 4 2 0 0 0 0 0 0 2 ...
## ..$ SRR11550000: int [1:58302] 0 1 3 0 0 0 0 0 0 0 ...
## ..$ SRR11550003: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR11550004: int [1:58302] 0 2 0 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11549999: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550000: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550003: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550004: 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:
## ..$ SRR11549999: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550000: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550003: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550004: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "WARN(3,4,6)" "WARN(3,4,6)"
## ..$ SRX_accession: chr [1:4] "SRX8119755" "SRX8119756" "SRX8119759" "SRX8119760"
## ..$ SRS_accession: chr [1:4] "SRS6484360" "SRS6484361" "SRS6484364" "SRS6484365"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477916" "GSM4477917" "GSM4477920" "GSM4477921"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "WARN(3,4,6)" "WARN(3,4,6)"
## ..$ SRX_accession : chr [1:4] "SRX8119755" "SRX8119756" "SRX8119759" "SRX8119760"
## ..$ SRS_accession : chr [1:4] "SRS6484360" "SRS6484361" "SRS6484364" "SRS6484365"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477916" "GSM4477917" "GSM4477920" "GSM4477921"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477916" "GSM4477917" "GSM4477920" "GSM4477921"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:13:13" "2020-04-15 14:15:26" "2020-04-15 14:17:36" "2020-04-15 14:18:36"
## ..$ spots : int [1:4] 16689791 17520017 27573490 23872357
## ..$ bases : int [1:4] 1268424116 1331521292 2095585240 1814299132
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 465 478 738 645
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra75/SRR/011279/SRR11549999" "https://sra-download.ncbi.nlm.nih.gov/traces/sra74/SRR/011279/SRR11550000" "https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011279/SRR11550003" "https://sra-download.ncbi.nlm.nih.gov/traces/sra60/SRR/011279/SRR11550004"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484360" "SRS6484361" "SRS6484364" "SRS6484365"
## ..$ BioSample : chr [1:4] "SAMN14602061" "SAMN14602060" "SAMN14602041" "SAMN14602040"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "650F29C7F837170003E35A519A4BCF97" "22D94DE04FFB9A3FCBC7532FED779E8D" "2AA159FBE58C38063442ACCE1F8A6D36" "1C27DC70932994AD2655DC5EAEBC1FF5"
## ..$ ReadHash : chr [1:4] "19AB89BFCEA4679F97BC34DA2E341B5C" "049FF2155DADA5D9126E8D5222A52A17" "D8F4A50C5521B7864DF82B443094C03D" "561E89B4EA52F199827F1DC3555D9371"
## $ 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
## SRP256479: Series 2 Calu3 cells mock treatment versus infected with SARS-CoV-1 4 hours post infection: mock;SRX8119761,SRX8119762: SARS-CoV-1;SRX8119763,SRX8119764;## 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:
## ..$ SRR11550005: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550006: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11550007: int [1:58302] 0 2 2 0 0 0 0 0 0 0 ...
## ..$ SRR11550008: int [1:58302] 0 0 2 0 0 0 0 0 0 2 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11550005: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550006: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550007: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550008: 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:
## ..$ SRR11550005: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550006: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550007: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550008: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "WARN(1,4,5,7)" "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119761" "SRX8119762" "SRX8119763" "SRX8119764"
## ..$ SRS_accession: chr [1:4] "SRS6484366" "SRS6484367" "SRS6484368" "SRS6484369"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477922" "GSM4477923" "GSM4477924" "GSM4477925"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "WARN(1,4,5,7)" "PASS" "PASS" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119761" "SRX8119762" "SRX8119763" "SRX8119764"
## ..$ SRS_accession : chr [1:4] "SRS6484366" "SRS6484367" "SRS6484368" "SRS6484369"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477922" "GSM4477923" "GSM4477924" "GSM4477925"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477922" "GSM4477923" "GSM4477924" "GSM4477925"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:11:38" "2020-04-15 14:14:50" "2020-04-15 14:16:21" "2020-04-15 14:15:00"
## ..$ spots : int [1:4] 7066831 19274597 17594551 16875234
## ..$ bases : int [1:4] 537079156 1464869372 1337185876 1282517784
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 195 520 476 457
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/011279/SRR11550005" "https://sra-download.ncbi.nlm.nih.gov/traces/sra71/SRR/011279/SRR11550006" "https://sra-download.ncbi.nlm.nih.gov/traces/sra78/SRR/011279/SRR11550007" "https://sra-download.ncbi.nlm.nih.gov/traces/sra8/SRR/011279/SRR11550008"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484366" "SRS6484367" "SRS6484368" "SRS6484369"
## ..$ BioSample : chr [1:4] "SAMN14602039" "SAMN14602038" "SAMN14602037" "SAMN14602036"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "7D7938B2AD1078CF5B01C5B9943EC286" "040FF10543EC38527AFDB2C90B3FE9CD" "CA3FFA0493C4D3D7084C9BEEA69FDED3" "3809A5269ED67FED0CF36F716A940D3B"
## ..$ ReadHash : chr [1:4] "9358479F85FEF79A731AF8224E0771D8" "29B11BEFA1E1CA56504E39694E874C42" "958EAE479787C48FFC580A963F76F179" "40BE59B0DA187C28A5BE563B77E607B3"
## $ 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
## SRP256479: Series 2 Calu3 cells mock treatment versus infected with SARS-CoV-2 4 hours post infection: mock;SRX8119761,SRX8119762: SARS-CoV-2;SRX8119765,SRX8119766;## 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:
## ..$ SRR11550005: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550006: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11550009: int [1:58302] 0 2 4 0 0 0 0 0 0 1 ...
## ..$ SRR11550010: int [1:58302] 0 2 2 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11550005: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550006: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550009: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550010: 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:
## ..$ SRR11550005: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550006: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550009: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550010: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "WARN(1,4,5,7)" "PASS" "PASS" "PASS"
## ..$ SRX_accession: chr [1:4] "SRX8119761" "SRX8119762" "SRX8119765" "SRX8119766"
## ..$ SRS_accession: chr [1:4] "SRS6484366" "SRS6484367" "SRS6484370" "SRS6484371"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477922" "GSM4477923" "GSM4477926" "GSM4477927"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "WARN(1,4,5,7)" "PASS" "PASS" "PASS"
## ..$ SRX_accession : chr [1:4] "SRX8119761" "SRX8119762" "SRX8119765" "SRX8119766"
## ..$ SRS_accession : chr [1:4] "SRS6484366" "SRS6484367" "SRS6484370" "SRS6484371"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477922" "GSM4477923" "GSM4477926" "GSM4477927"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477922" "GSM4477923" "GSM4477926" "GSM4477927"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:11:38" "2020-04-15 14:14:50" "2020-04-15 14:15:39" "2020-04-15 14:16:47"
## ..$ spots : int [1:4] 7066831 19274597 24407750 22825048
## ..$ bases : int [1:4] 537079156 1464869372 1854989000 1734703648
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 76 76 76 76
## ..$ size_MB : int [1:4] 195 520 671 612
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/011279/SRR11550005" "https://sra-download.ncbi.nlm.nih.gov/traces/sra71/SRR/011279/SRR11550006" "https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011279/SRR11550009" "https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/011279/SRR11550010"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484366" "SRS6484367" "SRS6484370" "SRS6484371"
## ..$ BioSample : chr [1:4] "SAMN14602039" "SAMN14602038" "SAMN14602035" "SAMN14602034"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "7D7938B2AD1078CF5B01C5B9943EC286" "040FF10543EC38527AFDB2C90B3FE9CD" "D2CCB319DC5F8F4AFC334079DBE1AD0D" "14B6CBB17BD796135A04745ED5A8409F"
## ..$ ReadHash : chr [1:4] "9358479F85FEF79A731AF8224E0771D8" "29B11BEFA1E1CA56504E39694E874C42" "2305B48C1627BF4026B8D77D07A1D9C6" "AB020DF66EA5480DC96020F91C2CEAEE"
## $ 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
## SRP256479: Series 2 Calu3 cells mock treatment (4 and 12 hrs) versus infected with SARS-CoV-1 8 hours post infection: mock;SRX8119761,SRX8119762,SRX8119755,SRX8119756: SARS-CoV-1;SRX8119767,SRX8119768;## 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:
## ..$ SRR11549999: int [1:58302] 1 4 2 0 0 0 0 0 0 2 ...
## ..$ SRR11550000: int [1:58302] 0 1 3 0 0 0 0 0 0 0 ...
## ..$ SRR11550005: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550006: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11550011: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR11550012: int [1:58302] 0 0 3 0 0 0 0 0 0 3 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549999: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550000: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550005: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550006: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550011: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550012: 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:
## ..$ SRR11549999: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550000: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550005: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550006: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550011: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550012: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "WARN(1,4,5,7)" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119755" "SRX8119756" "SRX8119761" "SRX8119762" ...
## ..$ SRS_accession: chr [1:6] "SRS6484360" "SRS6484361" "SRS6484366" "SRS6484367" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477916" "GSM4477917" "GSM4477922" "GSM4477923" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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" "WARN(1,4,5,7)" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX8119755" "SRX8119756" "SRX8119761" "SRX8119762" ...
## ..$ SRS_accession : chr [1:6] "SRS6484360" "SRS6484361" "SRS6484366" "SRS6484367" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477916" "GSM4477917" "GSM4477922" "GSM4477923" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477916" "GSM4477917" "GSM4477922" "GSM4477923" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 14:13:13" "2020-04-15 14:15:26" "2020-04-15 14:11:38" "2020-04-15 14:14:50" ...
## ..$ spots : int [1:6] 16689791 17520017 7066831 19274597 20536283 19234547
## ..$ bases : int [1:6] 1268424116 1331521292 537079156 1464869372 1560757508 1461825572
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 465 478 195 520 554 518
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra75/SRR/011279/SRR11549999" "https://sra-download.ncbi.nlm.nih.gov/traces/sra74/SRR/011279/SRR11550000" "https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/011279/SRR11550005" "https://sra-download.ncbi.nlm.nih.gov/traces/sra71/SRR/011279/SRR11550006" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484360" "SRS6484361" "SRS6484366" "SRS6484367" ...
## ..$ BioSample : chr [1:6] "SAMN14602061" "SAMN14602060" "SAMN14602039" "SAMN14602038" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "650F29C7F837170003E35A519A4BCF97" "22D94DE04FFB9A3FCBC7532FED779E8D" "7D7938B2AD1078CF5B01C5B9943EC286" "040FF10543EC38527AFDB2C90B3FE9CD" ...
## ..$ ReadHash : chr [1:6] "19AB89BFCEA4679F97BC34DA2E341B5C" "049FF2155DADA5D9126E8D5222A52A17" "9358479F85FEF79A731AF8224E0771D8" "29B11BEFA1E1CA56504E39694E874C42" ...
## $ 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
## SRP256479: Series 2 Calu3 cells mock treatment (4 and 12 hrs) versus infected with SARS-CoV-2 8 hours post infection: mock;SRX8119761,SRX8119762,SRX8119755,SRX8119756: SARS-CoV-2;SRX8119769,SRX8119770;## 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:
## ..$ SRR11549999: int [1:58302] 1 4 2 0 0 0 0 0 0 2 ...
## ..$ SRR11550000: int [1:58302] 0 1 3 0 0 0 0 0 0 0 ...
## ..$ SRR11550005: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550006: int [1:58302] 0 1 1 0 0 0 0 0 0 0 ...
## ..$ SRR11550013: int [1:58302] 1 0 3 0 0 0 0 0 0 4 ...
## ..$ SRR11550014: int [1:58302] 0 2 4 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR11549999: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550000: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550005: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550006: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550013: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550014: 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:
## ..$ SRR11549999: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550000: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550005: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550006: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550013: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550014: chr [1:30] "SE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "WARN(1,4,5,7)" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX8119755" "SRX8119756" "SRX8119761" "SRX8119762" ...
## ..$ SRS_accession: chr [1:6] "SRS6484360" "SRS6484361" "SRS6484366" "SRS6484367" ...
## ..$ SRP_accession: chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477916" "GSM4477917" "GSM4477922" "GSM4477923" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ 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" "WARN(1,4,5,7)" "PASS" ...
## ..$ SRX_accession : chr [1:6] "SRX8119755" "SRX8119756" "SRX8119761" "SRX8119762" ...
## ..$ SRS_accession : chr [1:6] "SRS6484360" "SRS6484361" "SRS6484366" "SRS6484367" ...
## ..$ SRP_accession : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ Sample_name : chr [1:6] "GSM4477916" "GSM4477917" "GSM4477922" "GSM4477923" ...
## ..$ GEO_series : chr [1:6] "GSE148729" "GSE148729" "GSE148729" "GSE148729" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4477916" "GSM4477917" "GSM4477922" "GSM4477923" ...
## ..$ ReleaseDate : chr [1:6] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" ...
## ..$ LoadDate : chr [1:6] "2020-04-15 14:13:13" "2020-04-15 14:15:26" "2020-04-15 14:11:38" "2020-04-15 14:14:50" ...
## ..$ spots : int [1:6] 16689791 17520017 7066831 19274597 27200369 26103647
## ..$ bases : int [1:6] 1268424116 1331521292 537079156 1464869372 2067228044 1983877172
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 76 76 76 76 76 76
## ..$ size_MB : int [1:6] 465 478 195 520 731 701
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra75/SRR/011279/SRR11549999" "https://sra-download.ncbi.nlm.nih.gov/traces/sra74/SRR/011279/SRR11550000" "https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/011279/SRR11550005" "https://sra-download.ncbi.nlm.nih.gov/traces/sra71/SRR/011279/SRR11550006" ...
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:6] "SRP256479" "SRP256479" "SRP256479" "SRP256479" ...
## ..$ BioProject : chr [1:6] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 625518 625518 625518 625518 625518 625518
## ..$ Sample : chr [1:6] "SRS6484360" "SRS6484361" "SRS6484366" "SRS6484367" ...
## ..$ BioSample : chr [1:6] "SAMN14602061" "SAMN14602060" "SAMN14602039" "SAMN14602038" ...
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "650F29C7F837170003E35A519A4BCF97" "22D94DE04FFB9A3FCBC7532FED779E8D" "7D7938B2AD1078CF5B01C5B9943EC286" "040FF10543EC38527AFDB2C90B3FE9CD" ...
## ..$ ReadHash : chr [1:6] "19AB89BFCEA4679F97BC34DA2E341B5C" "049FF2155DADA5D9126E8D5222A52A17" "9358479F85FEF79A731AF8224E0771D8" "29B11BEFA1E1CA56504E39694E874C42" ...
## $ 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
## SRP256479: Calu3 cells mock treatment versus infected with SARS-CoV-1 24 hours post infection (smallRNA): mock;SRX8119771,SRX8119772: SARS-CoV-1;SRX8119777,SRX8119778;## 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:
## ..$ SRR11550015: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550016: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550021: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550022: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11550015: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550016: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550021: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550022: 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:
## ..$ SRR11550015: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550016: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550021: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550022: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)"
## ..$ SRX_accession: chr [1:4] "SRX8119771" "SRX8119772" "SRX8119777" "SRX8119778"
## ..$ SRS_accession: chr [1:4] "SRS6484376" "SRS6484377" "SRS6484382" "SRS6484383"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477932" "GSM4477933" "GSM4477938" "GSM4477939"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)"
## ..$ SRX_accession : chr [1:4] "SRX8119771" "SRX8119772" "SRX8119777" "SRX8119778"
## ..$ SRS_accession : chr [1:4] "SRS6484376" "SRS6484377" "SRS6484382" "SRS6484383"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477932" "GSM4477933" "GSM4477938" "GSM4477939"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477932" "GSM4477933" "GSM4477938" "GSM4477939"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:13:35" "2020-04-15 14:14:42" "2020-04-15 14:15:39" "2020-04-15 14:16:14"
## ..$ spots : int [1:4] 8987403 13496254 13709754 15770452
## ..$ bases : int [1:4] 458357553 688308954 699197454 804293052
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 51 51 51 51
## ..$ size_MB : int [1:4] 194 292 299 343
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra68/SRR/011279/SRR11550015" "https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/011279/SRR11550016" "https://sra-download.ncbi.nlm.nih.gov/traces/sra28/SRR/011279/SRR11550021" "https://sra-download.ncbi.nlm.nih.gov/traces/sra66/SRR/011279/SRR11550022"
## ..$ LibraryName : logi [1:4] NA NA NA NA
## ..$ LibraryStrategy : chr [1:4] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq"
## ..$ LibrarySelection : chr [1:4] "size fractionation" "size fractionation" "size fractionation" "size fractionation"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484376" "SRS6484377" "SRS6484382" "SRS6484383"
## ..$ BioSample : chr [1:4] "SAMN14602029" "SAMN14602028" "SAMN14602082" "SAMN14602081"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "B287CEE2A5E461A473B4158AC0D15ED6" "1CC4CD7B831B095C90B2690E92551630" "3B9C7F146528A3E88525A1EDB30871BD" "6F037BA75F686606C997E1DB5D65634D"
## ..$ ReadHash : chr [1:4] "67916B9DEA7E985867BC92CAEF54E46B" "C35361195FABF8691A8056B844FDB4DB" "3AA900935015D18FEE69168813674039" "955E602B1C508175ECDDA3B9E344B1DD"
## $ absent : chr(0)## SRP256479: Calu3 cells mock treatment versus infected with SARS-CoV-1 4 hours post infection (smallRNA): mock;SRX8119773,SRX8119774: SARS-CoV-1;SRX8119779,SRX8119780;
## 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:
## ..$ SRR11550017: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550018: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550023: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550024: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11550017: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550018: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550023: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550024: 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:
## ..$ SRR11550017: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550018: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550023: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550024: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "FAIL(3,4,5,6)" "FAIL(3,4,5,6)" "FAIL(3,4,5,6)" "FAIL(3,4,5,6)"
## ..$ SRX_accession: chr [1:4] "SRX8119773" "SRX8119774" "SRX8119779" "SRX8119780"
## ..$ SRS_accession: chr [1:4] "SRS6484378" "SRS6484379" "SRS6484384" "SRS6484385"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477934" "GSM4477935" "GSM4477940" "GSM4477941"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "FAIL(3,4,5,6)" "FAIL(3,4,5,6)" "FAIL(3,4,5,6)" "FAIL(3,4,5,6)"
## ..$ SRX_accession : chr [1:4] "SRX8119773" "SRX8119774" "SRX8119779" "SRX8119780"
## ..$ SRS_accession : chr [1:4] "SRS6484378" "SRS6484379" "SRS6484384" "SRS6484385"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477934" "GSM4477935" "GSM4477940" "GSM4477941"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477934" "GSM4477935" "GSM4477940" "GSM4477941"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:15:48" "2020-04-15 14:16:36" "2020-04-15 14:18:26" "2020-04-15 14:17:54"
## ..$ spots : int [1:4] 16986510 17688944 14617841 18626610
## ..$ bases : int [1:4] 866312010 902136144 745509891 949957110
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 51 51 51 51
## ..$ size_MB : int [1:4] 366 382 315 403
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/011279/SRR11550017" "https://sra-download.ncbi.nlm.nih.gov/traces/sra66/SRR/011279/SRR11550018" "https://sra-download.ncbi.nlm.nih.gov/traces/sra51/SRR/011279/SRR11550023" "https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRR/011279/SRR11550024"
## ..$ LibraryName : logi [1:4] NA NA NA NA
## ..$ LibraryStrategy : chr [1:4] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq"
## ..$ LibrarySelection : chr [1:4] "size fractionation" "size fractionation" "size fractionation" "size fractionation"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484378" "SRS6484379" "SRS6484384" "SRS6484385"
## ..$ BioSample : chr [1:4] "SAMN14602027" "SAMN14602085" "SAMN14602080" "SAMN14602152"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "8DAE4AB8356FE49220C83EFDB5140910" "25FE24A2AD9A62DD6692E9159FDBA20A" "1323FCFC69F2FA6ECFAD3A9E610F3C12" "C00272A3E2CC39BB9C94EFFACFA470A2"
## ..$ ReadHash : chr [1:4] "AE2F37554F0264A5D20ACCF0A5EBE13E" "8CCF6CBB2D34AC30B6F8C25A6089985E" "908CF993149547F0CED015B7CF46AA4F" "001D08858416F2CBEF14DF6FC5C8EA3C"
## $ absent : chr(0)## SRP256479: Calu3 cells mock treatment versus infected with SARS-CoV-2 24 hours post infection (smallRNA): mock;SRX8119771,SRX8119772: SARS-CoV-2;SRX8119783,SRX8119784;
## 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:
## ..$ SRR11550015: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550016: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550027: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550028: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11550015: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550016: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550027: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550028: 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:
## ..$ SRR11550015: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550016: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550027: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550028: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6)" "FAIL(3,4,5,6)"
## ..$ SRX_accession: chr [1:4] "SRX8119771" "SRX8119772" "SRX8119783" "SRX8119784"
## ..$ SRS_accession: chr [1:4] "SRS6484376" "SRS6484377" "SRS6484388" "SRS6484389"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477932" "GSM4477933" "GSM4477944" "GSM4477945"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6)" "FAIL(3,4,5,6)"
## ..$ SRX_accession : chr [1:4] "SRX8119771" "SRX8119772" "SRX8119783" "SRX8119784"
## ..$ SRS_accession : chr [1:4] "SRS6484376" "SRS6484377" "SRS6484388" "SRS6484389"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477932" "GSM4477933" "GSM4477944" "GSM4477945"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477932" "GSM4477933" "GSM4477944" "GSM4477945"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:13:35" "2020-04-15 14:14:42" "2020-04-15 14:18:37" "2020-04-15 14:19:16"
## ..$ spots : int [1:4] 8987403 13496254 22767189 21129791
## ..$ bases : int [1:4] 458357553 688308954 1161126639 1077619341
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 51 51 51 51
## ..$ size_MB : int [1:4] 194 292 491 455
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra68/SRR/011279/SRR11550015" "https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/011279/SRR11550016" "https://sra-download.ncbi.nlm.nih.gov/traces/sra80/SRR/011279/SRR11550027" "https://sra-download.ncbi.nlm.nih.gov/traces/sra73/SRR/011279/SRR11550028"
## ..$ LibraryName : logi [1:4] NA NA NA NA
## ..$ LibraryStrategy : chr [1:4] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq"
## ..$ LibrarySelection : chr [1:4] "size fractionation" "size fractionation" "size fractionation" "size fractionation"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484376" "SRS6484377" "SRS6484388" "SRS6484389"
## ..$ BioSample : chr [1:4] "SAMN14602029" "SAMN14602028" "SAMN14602079" "SAMN14602078"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "B287CEE2A5E461A473B4158AC0D15ED6" "1CC4CD7B831B095C90B2690E92551630" "B633358A4BB8EBA633F956326F0DCEC2" "AC6301E1182454649356B1B28CFDA4E8"
## ..$ ReadHash : chr [1:4] "67916B9DEA7E985867BC92CAEF54E46B" "C35361195FABF8691A8056B844FDB4DB" "0BE1E386D1CA6D1305E198EE72B4F09F" "22234DA9D02B70BFEAE302D3BADE6AD4"
## $ absent : chr(0)## SRP256479: Calu3 cells mock treatment versus infected with SARS-CoV-2 4 hours post infection (smallRNA): mock;SRX8119773,SRX8119774: SARS-CoV-2;SRX8119785,SRX8119786;
## 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:
## ..$ SRR11550017: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550018: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550029: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550030: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11550017: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550018: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550029: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550030: 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:
## ..$ SRR11550017: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550018: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550029: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR11550030: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "FAIL(3,4,5,6)" "FAIL(3,4,5,6)" "FAIL(3,4,5,6)" "FAIL(3,4,5,6)"
## ..$ SRX_accession: chr [1:4] "SRX8119773" "SRX8119774" "SRX8119785" "SRX8119786"
## ..$ SRS_accession: chr [1:4] "SRS6484378" "SRS6484379" "SRS6484390" "SRS6484391"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477934" "GSM4477935" "GSM4477946" "GSM4477947"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "FAIL(3,4,5,6)" "FAIL(3,4,5,6)" "FAIL(3,4,5,6)" "FAIL(3,4,5,6)"
## ..$ SRX_accession : chr [1:4] "SRX8119773" "SRX8119774" "SRX8119785" "SRX8119786"
## ..$ SRS_accession : chr [1:4] "SRS6484378" "SRS6484379" "SRS6484390" "SRS6484391"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477934" "GSM4477935" "GSM4477946" "GSM4477947"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477934" "GSM4477935" "GSM4477946" "GSM4477947"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:15:48" "2020-04-15 14:16:36" "2020-04-15 14:16:23" "2020-04-15 14:18:09"
## ..$ spots : int [1:4] 16986510 17688944 11450978 15715237
## ..$ bases : int [1:4] 866312010 902136144 583999878 801477087
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 51 51 51 51
## ..$ size_MB : int [1:4] 366 382 247 340
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/011279/SRR11550017" "https://sra-download.ncbi.nlm.nih.gov/traces/sra66/SRR/011279/SRR11550018" "https://sra-download.ncbi.nlm.nih.gov/traces/sra61/SRR/011279/SRR11550029" "https://sra-download.ncbi.nlm.nih.gov/traces/sra80/SRR/011279/SRR11550030"
## ..$ LibraryName : logi [1:4] NA NA NA NA
## ..$ LibraryStrategy : chr [1:4] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq"
## ..$ LibrarySelection : chr [1:4] "size fractionation" "size fractionation" "size fractionation" "size fractionation"
## ..$ 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] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500"
## ..$ SRAStudy : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484378" "SRS6484379" "SRS6484390" "SRS6484391"
## ..$ BioSample : chr [1:4] "SAMN14602027" "SAMN14602085" "SAMN14602110" "SAMN14602109"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "8DAE4AB8356FE49220C83EFDB5140910" "25FE24A2AD9A62DD6692E9159FDBA20A" "83376D76B9AE4C52FF63AED9654B90D0" "051C4A033C6B5417E3F6745DB2FFC881"
## ..$ ReadHash : chr [1:4] "AE2F37554F0264A5D20ACCF0A5EBE13E" "8CCF6CBB2D34AC30B6F8C25A6089985E" "08EF04915E9918072859E5024ED5A479" "F25FC325AE5C8DB45178B70D6C334673"
## $ absent : chr(0)## SRP256479: Calu3 cells mock treatment versus infected with SARS-CoV-1 24 hours post infection (totalRNA): mock; SRX8119789, SRX8119790: SARS-CoV-1;SRX8119795,SRX8119796;
## 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 2 variables:
## ..$ SRR11550039: int [1:58302] 0 0 1 0 0 0 0 0 0 2 ...
## ..$ SRR11550040: int [1:58302] 0 5 1 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 2 variables:
## ..$ SRR11550039: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550040: 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 2 variables:
## ..$ SRR11550039: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550040: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 2 obs. of 7 variables:
## ..$ QC_summary : chr [1:2] "FAIL(3,4,6)" "FAIL(3,4,6)"
## ..$ SRX_accession: chr [1:2] "SRX8119795" "SRX8119796"
## ..$ SRS_accession: chr [1:2] "SRS6484400" "SRS6484401"
## ..$ SRP_accession: chr [1:2] "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:2] "GSM4477956" "GSM4477957"
## ..$ GEO_series : chr [1:2] "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:2] NA NA
## $ MetadataFull :'data.frame': 2 obs. of 52 variables:
## ..$ QC_summary : chr [1:2] "FAIL(3,4,6)" "FAIL(3,4,6)"
## ..$ SRX_accession : chr [1:2] "SRX8119795" "SRX8119796"
## ..$ SRS_accession : chr [1:2] "SRS6484400" "SRS6484401"
## ..$ SRP_accession : chr [1:2] "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:2] "GSM4477956" "GSM4477957"
## ..$ GEO_series : chr [1:2] "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:2] NA NA
## ..$ SampleName : chr [1:2] "GSM4477956" "GSM4477957"
## ..$ ReleaseDate : chr [1:2] "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:2] "2020-04-15 14:23:31" "2020-04-15 14:23:09"
## ..$ spots : int [1:2] 17934396 17815575
## ..$ bases : num [1:2] 2.73e+09 2.71e+09
## ..$ spots_with_mates : int [1:2] 17934396 17815575
## ..$ avgLength : int [1:2] 152 152
## ..$ size_MB : int [1:2] 919 1033
## ..$ AssemblyName : logi [1:2] NA NA
## ..$ download_path : chr [1:2] "https://sra-download.ncbi.nlm.nih.gov/traces/sra73/SRR/011279/SRR11550039" "https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/011279/SRR11550040"
## ..$ LibraryName : logi [1:2] NA NA
## ..$ LibraryStrategy : chr [1:2] "RNA-Seq" "RNA-Seq"
## ..$ LibrarySelection : chr [1:2] "cDNA" "cDNA"
## ..$ LibrarySource : chr [1:2] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr [1:2] "PAIRED" "PAIRED"
## ..$ InsertSize : int [1:2] 0 0
## ..$ InsertDev : num [1:2] 0 0
## ..$ Platform : chr [1:2] "ILLUMINA" "ILLUMINA"
## ..$ Model : chr [1:2] "Illumina HiSeq 4000" "Illumina HiSeq 4000"
## ..$ SRAStudy : chr [1:2] "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:2] "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:2] NA NA
## ..$ ProjectID : int [1:2] 625518 625518
## ..$ Sample : chr [1:2] "SRS6484400" "SRS6484401"
## ..$ BioSample : chr [1:2] "SAMN14602141" "SAMN14602140"
## ..$ SampleType : chr [1:2] "simple" "simple"
## ..$ TaxID : int [1:2] 9606 9606
## ..$ ScientificName : chr [1:2] "Homo sapiens" "Homo sapiens"
## ..$ g1k_pop_code : logi [1:2] NA NA
## ..$ source : logi [1:2] NA NA
## ..$ g1k_analysis_group : logi [1:2] NA NA
## ..$ Subject_ID : logi [1:2] NA NA
## ..$ Sex : logi [1:2] NA NA
## ..$ Disease : logi [1:2] NA NA
## ..$ Tumor : chr [1:2] "no" "no"
## ..$ Affection_Status : logi [1:2] NA NA
## ..$ Analyte_Type : logi [1:2] NA NA
## ..$ Histological_Type : logi [1:2] NA NA
## ..$ Body_Site : logi [1:2] NA NA
## ..$ CenterName : chr [1:2] "GEO" "GEO"
## ..$ Submission : chr [1:2] "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:2] NA NA
## ..$ Consent : chr [1:2] "public" "public"
## ..$ RunHash : chr [1:2] "1A139FA8DBA4AD9BC6DEAAB2E66D4665" "511022FFE1229E31DAADE869A0053C39"
## ..$ ReadHash : chr [1:2] "69A9313095A92E751A4D37817DC982A7" "A2C55D3AC1B1BD5CDBF6AC416B53995C"
## $ absent : chr(0)## SRP256479: Calu3 cells mock treatment versus infected with SARS-CoV-1 4 hours post infection (totalRNA): mock;SRX8119791,SRX8119792: SARS-CoV-1;SRX8119797,SRX8119798;
## 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:
## ..$ SRR11550035: int [1:58302] 0 9 1 0 0 0 0 0 0 3 ...
## ..$ SRR11550036: int [1:58302] 1 19 2 0 0 0 0 0 0 1 ...
## ..$ SRR11550041: int [1:58302] 0 11 0 0 0 0 0 0 0 3 ...
## ..$ SRR11550042: int [1:58302] 0 28 2 0 0 0 0 0 0 2 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11550035: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550036: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550041: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550042: 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:
## ..$ SRR11550035: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550036: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550041: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550042: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "WARN(5,7,8)" "WARN(5,8)" "WARN(3,4,5,6,7)" "WARN(5,8)"
## ..$ SRX_accession: chr [1:4] "SRX8119791" "SRX8119792" "SRX8119797" "SRX8119798"
## ..$ SRS_accession: chr [1:4] "SRS6484396" "SRS6484397" "SRS6484402" "SRS6484403"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477952" "GSM4477953" "GSM4477958" "GSM4477959"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "WARN(5,7,8)" "WARN(5,8)" "WARN(3,4,5,6,7)" "WARN(5,8)"
## ..$ SRX_accession : chr [1:4] "SRX8119791" "SRX8119792" "SRX8119797" "SRX8119798"
## ..$ SRS_accession : chr [1:4] "SRS6484396" "SRS6484397" "SRS6484402" "SRS6484403"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477952" "GSM4477953" "GSM4477958" "GSM4477959"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477952" "GSM4477953" "GSM4477958" "GSM4477959"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:00"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:19:51" "2020-04-15 14:22:29" "2020-04-15 14:22:16" "2020-04-15 14:21:26"
## ..$ spots : int [1:4] 13056540 15255046 14578050 15790867
## ..$ bases : num [1:4] 1.98e+09 2.32e+09 2.22e+09 2.40e+09
## ..$ spots_with_mates : int [1:4] 13056540 15255046 14578050 15790867
## ..$ avgLength : int [1:4] 152 152 152 152
## ..$ size_MB : int [1:4] 681 786 759 815
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra75/SRR/011279/SRR11550035" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/011279/SRR11550036" "https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/011279/SRR11550041" "https://sra-download.ncbi.nlm.nih.gov/traces/sra11/SRR/011279/SRR11550042"
## ..$ 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] "PAIRED" "PAIRED" "PAIRED" "PAIRED"
## ..$ 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] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484396" "SRS6484397" "SRS6484402" "SRS6484403"
## ..$ BioSample : chr [1:4] "SAMN14602145" "SAMN14602144" "SAMN14602139" "SAMN14602138"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "19B48FC2A788ADBAADFF0565E8E15FA5" "FB250201321CC3BE2939AF833381C7CF" "91345D1E4B6574871BAA127D5B1FE1B6" "46F5BFA8D3FC8FFC36ED3E94EB0809A2"
## ..$ ReadHash : chr [1:4] "2C9D9C0A6039BB93E4636E784AC9E353" "E75E4366E72FF33789481FA0AAB9354B" "273001707CC6E7838736744525B93EB6" "1C4657C46E2AC88281A117AC404374F5"
## $ 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
## SRP256479: Calu3 cells mock treatment versus infected with SARS-CoV-2 24 hours post infection (totalRNA): mock; SRX8119789, SRX8119790: SARS-CoV-2;SRX8119801,SRX8119802;## 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 2 variables:
## ..$ SRR11550045: int [1:58302] 0 6 0 0 0 0 0 0 0 3 ...
## ..$ SRR11550046: int [1:58302] 0 9 0 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 2 variables:
## ..$ SRR11550045: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550046: 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 2 variables:
## ..$ SRR11550045: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550046: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 2 obs. of 7 variables:
## ..$ QC_summary : chr [1:2] "FAIL(3,4,6)" "FAIL(3,4,6)"
## ..$ SRX_accession: chr [1:2] "SRX8119801" "SRX8119802"
## ..$ SRS_accession: chr [1:2] "SRS6484406" "SRS6484407"
## ..$ SRP_accession: chr [1:2] "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:2] "GSM4477962" "GSM4477963"
## ..$ GEO_series : chr [1:2] "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:2] NA NA
## $ MetadataFull :'data.frame': 2 obs. of 52 variables:
## ..$ QC_summary : chr [1:2] "FAIL(3,4,6)" "FAIL(3,4,6)"
## ..$ SRX_accession : chr [1:2] "SRX8119801" "SRX8119802"
## ..$ SRS_accession : chr [1:2] "SRS6484406" "SRS6484407"
## ..$ SRP_accession : chr [1:2] "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:2] "GSM4477962" "GSM4477963"
## ..$ GEO_series : chr [1:2] "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:2] NA NA
## ..$ SampleName : chr [1:2] "GSM4477962" "GSM4477963"
## ..$ ReleaseDate : chr [1:2] "2020-05-05 09:32:01" "2020-05-05 09:32:01"
## ..$ LoadDate : chr [1:2] "2020-04-15 14:22:52" "2020-04-15 14:24:14"
## ..$ spots : int [1:2] 15281469 17059697
## ..$ bases : num [1:2] 2.32e+09 2.59e+09
## ..$ spots_with_mates : int [1:2] 15281469 17059697
## ..$ avgLength : int [1:2] 152 152
## ..$ size_MB : int [1:2] 779 874
## ..$ AssemblyName : logi [1:2] NA NA
## ..$ download_path : chr [1:2] "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/011279/SRR11550045" "https://sra-download.ncbi.nlm.nih.gov/traces/sra78/SRR/011279/SRR11550046"
## ..$ LibraryName : logi [1:2] NA NA
## ..$ LibraryStrategy : chr [1:2] "RNA-Seq" "RNA-Seq"
## ..$ LibrarySelection : chr [1:2] "cDNA" "cDNA"
## ..$ LibrarySource : chr [1:2] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr [1:2] "PAIRED" "PAIRED"
## ..$ InsertSize : int [1:2] 0 0
## ..$ InsertDev : num [1:2] 0 0
## ..$ Platform : chr [1:2] "ILLUMINA" "ILLUMINA"
## ..$ Model : chr [1:2] "Illumina HiSeq 4000" "Illumina HiSeq 4000"
## ..$ SRAStudy : chr [1:2] "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:2] "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:2] NA NA
## ..$ ProjectID : int [1:2] 625518 625518
## ..$ Sample : chr [1:2] "SRS6484406" "SRS6484407"
## ..$ BioSample : chr [1:2] "SAMN14602135" "SAMN14602134"
## ..$ SampleType : chr [1:2] "simple" "simple"
## ..$ TaxID : int [1:2] 9606 9606
## ..$ ScientificName : chr [1:2] "Homo sapiens" "Homo sapiens"
## ..$ g1k_pop_code : logi [1:2] NA NA
## ..$ source : logi [1:2] NA NA
## ..$ g1k_analysis_group : logi [1:2] NA NA
## ..$ Subject_ID : logi [1:2] NA NA
## ..$ Sex : logi [1:2] NA NA
## ..$ Disease : logi [1:2] NA NA
## ..$ Tumor : chr [1:2] "no" "no"
## ..$ Affection_Status : logi [1:2] NA NA
## ..$ Analyte_Type : logi [1:2] NA NA
## ..$ Histological_Type : logi [1:2] NA NA
## ..$ Body_Site : logi [1:2] NA NA
## ..$ CenterName : chr [1:2] "GEO" "GEO"
## ..$ Submission : chr [1:2] "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:2] NA NA
## ..$ Consent : chr [1:2] "public" "public"
## ..$ RunHash : chr [1:2] "C32D42910BBC2768B721FF372CD0216F" "C17451974AA053BBBB59CB781DA1DE44"
## ..$ ReadHash : chr [1:2] "5357C9F7076247E96A7AE4265C003508" "7032D3988487CDD30E6D379A8EECADA6"
## $ absent : chr(0)## SRP256479: Calu3 cells mock treatment versus infected with SARS-CoV-2 4 hours post infection (totalRNA): mock;SRX8119791,SRX8119792: SARS-CoV-2;SRX8119803,SRX8119804;
## 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:
## ..$ SRR11550035: int [1:58302] 0 9 1 0 0 0 0 0 0 3 ...
## ..$ SRR11550036: int [1:58302] 1 19 2 0 0 0 0 0 0 1 ...
## ..$ SRR11550047: int [1:58302] 0 22 2 0 0 0 0 0 0 3 ...
## ..$ SRR11550048: int [1:58302] 0 15 1 0 0 0 0 0 0 3 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR11550035: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550036: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550047: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR11550048: 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:
## ..$ SRR11550035: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550036: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550047: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## ..$ SRR11550048: chr [1:30] "PE" "Sanger/Illumina1.9" "76" "76" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "WARN(5,7,8)" "WARN(5,8)" "WARN(5,8)" "WARN(4,5,7,8)"
## ..$ SRX_accession: chr [1:4] "SRX8119791" "SRX8119792" "SRX8119803" "SRX8119804"
## ..$ SRS_accession: chr [1:4] "SRS6484396" "SRS6484397" "SRS6484408" "SRS6484409"
## ..$ SRP_accession: chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477952" "GSM4477953" "GSM4477964" "GSM4477965"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## $ MetadataFull :'data.frame': 4 obs. of 52 variables:
## ..$ QC_summary : chr [1:4] "WARN(5,7,8)" "WARN(5,8)" "WARN(5,8)" "WARN(4,5,7,8)"
## ..$ SRX_accession : chr [1:4] "SRX8119791" "SRX8119792" "SRX8119803" "SRX8119804"
## ..$ SRS_accession : chr [1:4] "SRS6484396" "SRS6484397" "SRS6484408" "SRS6484409"
## ..$ SRP_accession : chr [1:4] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ Sample_name : chr [1:4] "GSM4477952" "GSM4477953" "GSM4477964" "GSM4477965"
## ..$ GEO_series : chr [1:4] "GSE148729" "GSE148729" "GSE148729" "GSE148729"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM4477952" "GSM4477953" "GSM4477964" "GSM4477965"
## ..$ ReleaseDate : chr [1:4] "2020-05-05 09:32:00" "2020-05-05 09:32:00" "2020-05-05 09:32:01" "2020-05-05 09:32:01"
## ..$ LoadDate : chr [1:4] "2020-04-15 14:19:51" "2020-04-15 14:22:29" "2020-04-15 14:23:45" "2020-04-15 14:24:50"
## ..$ spots : int [1:4] 13056540 15255046 16011056 15418986
## ..$ bases : num [1:4] 1.98e+09 2.32e+09 2.43e+09 2.34e+09
## ..$ spots_with_mates : int [1:4] 13056540 15255046 16011056 15418986
## ..$ avgLength : int [1:4] 152 152 152 152
## ..$ size_MB : int [1:4] 681 786 834 800
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-download.ncbi.nlm.nih.gov/traces/sra75/SRR/011279/SRR11550035" "https://sra-download.ncbi.nlm.nih.gov/traces/sra72/SRR/011279/SRR11550036" "https://sra-download.ncbi.nlm.nih.gov/traces/sra80/SRR/011279/SRR11550047" "https://sra-download.ncbi.nlm.nih.gov/traces/sra2/SRR/011279/SRR11550048"
## ..$ 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] "PAIRED" "PAIRED" "PAIRED" "PAIRED"
## ..$ 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] "SRP256479" "SRP256479" "SRP256479" "SRP256479"
## ..$ BioProject : chr [1:4] "PRJNA625518" "PRJNA625518" "PRJNA625518" "PRJNA625518"
## ..$ Study_Pubmed_id : logi [1:4] NA NA NA NA
## ..$ ProjectID : int [1:4] 625518 625518 625518 625518
## ..$ Sample : chr [1:4] "SRS6484396" "SRS6484397" "SRS6484408" "SRS6484409"
## ..$ BioSample : chr [1:4] "SAMN14602145" "SAMN14602144" "SAMN14602175" "SAMN14602174"
## ..$ 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] "SRA1065617" "SRA1065617" "SRA1065617" "SRA1065617"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "19B48FC2A788ADBAADFF0565E8E15FA5" "FB250201321CC3BE2939AF833381C7CF" "02CBA0D863345B2E7002EA98684AFCEA" "DE9FA48DA43C32DAB54B86C89B86255A"
## ..$ ReadHash : chr [1:4] "2C9D9C0A6039BB93E4636E784AC9E353" "E75E4366E72FF33789481FA0AAB9354B" "1C17C0680D19C42C0B8032AD7402B14A" "34E446F8A1EE3F1A3DFB3E013A6A464F"
## $ 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
## SRP256479: DMSO mock infected versus SARS-CoV-2 infected cells: mock infected;SRX8784719,SRX8784720,SRX8784721,SRX8784728,SRX8784729,SRX8784730: SARS-CoV-2 infected;SRX8784722,SRX8784723,SRX8784724,SRX8784731,SRX8784732,SRX8784733;## Error. None of the specified SRR accessions are present.## NULL## SRP256479: DMSO mock infected versus 800 nM Onalespib treated SARS-CoV-2 infected cells: mock infected;SRX8784719,SRX8784720,SRX8784721,SRX8784728,SRX8784729,SRX8784730: Onalespib SARS-CoV-2 infected;SRX8784725,SRX8784726,SRX8784727;
## Error. None of the specified SRR accessions are present.## NULL## SRP256479: DMSO mock infected versus 800 nM 17-AAB treated SARS-CoV-2 infected cells: mock infected;SRX8784719,SRX8784720,SRX8784721,SRX8784728,SRX8784729,SRX8784730: 17-AAB SARS-CoV-2 infected;SRX8784734,SRX8784735,SRX8784736;
## Error. None of the specified SRR accessions are present.## NULL## SRP256479: DMSO mock infected versus 800 nM Ganetespib treated SARS-CoV-2 infected cells: mock infected;SRX8784719,SRX8784720,SRX8784721,SRX8784728,SRX8784729,SRX8784730: Ganetespib SARS-CoV-2 infected;SRX8784737,SRX8784738,SRX8784739;
## Error. None of the specified SRR accessions are present.## NULL## SRP227272: Calu-3 cells mock infection versus MERS-CoV 6 hours post infection (mRNA): mock;SRX7066767,SRX7066768,SRX7066769: 6 hours post infection;SRX7066770,SRX7066771,SRX7066772;## 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:
## ..$ SRR10357366: int [1:58302] 0 131 0 0 0 0 0 0 0 1 ...
## ..$ SRR10357367: int [1:58302] 0 80 0 0 0 0 0 0 0 1 ...
## ..$ SRR10357368: int [1:58302] 0 107 0 0 0 0 0 0 0 4 ...
## ..$ SRR10357369: int [1:58302] 0 120 1 0 0 0 0 0 0 4 ...
## ..$ SRR10357370: int [1:58302] 0 103 0 0 0 0 0 0 0 1 ...
## ..$ SRR10357371: int [1:58302] 0 118 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR10357366: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357367: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357368: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357369: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357370: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357371: 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:
## ..$ SRR10357366: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357367: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357368: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357369: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357370: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357371: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX7066767" "SRX7066768" "SRX7066769" "SRX7066770" ...
## ..$ SRS_accession: chr [1:6] "SRS5583369" "SRS5583370" "SRS5583371" "SRS5583372" ...
## ..$ SRP_accession: chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142814" "GSM4142815" "GSM4142816" "GSM4142817" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ 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] "SRX7066767" "SRX7066768" "SRX7066769" "SRX7066770" ...
## ..$ SRS_accession : chr [1:6] "SRS5583369" "SRS5583370" "SRS5583371" "SRS5583372" ...
## ..$ SRP_accession : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142814" "GSM4142815" "GSM4142816" "GSM4142817" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4142814" "GSM4142815" "GSM4142816" "GSM4142817" ...
## ..$ ReleaseDate : chr [1:6] "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" ...
## ..$ LoadDate : chr [1:6] "2019-10-28 17:50:22" "2019-10-28 17:46:06" "2019-10-28 17:47:07" "2019-10-28 17:43:57" ...
## ..$ spots : int [1:6] 31885169 22368064 23108924 20863811 19835626 22362375
## ..$ bases : num [1:6] 9.57e+09 6.71e+09 6.93e+09 6.26e+09 5.95e+09 ...
## ..$ spots_with_mates : int [1:6] 31885169 22368064 23108924 20863811 19835626 22362375
## ..$ avgLength : int [1:6] 300 300 300 300 300 300
## ..$ size_MB : int [1:6] 3767 2669 2761 2461 2326 2645
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/010114/SRR10357366" "https://sra-download.ncbi.nlm.nih.gov/traces/sra30/SRR/010114/SRR10357367" "https://sra-download.ncbi.nlm.nih.gov/traces/sra29/SRR/010114/SRR10357368" "https://sra-download.ncbi.nlm.nih.gov/traces/sra9/SRR/010114/SRR10357369" ...
## ..$ 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] "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" ...
## ..$ SRAStudy : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ BioProject : chr [1:6] "PRJNA580021" "PRJNA580021" "PRJNA580021" "PRJNA580021" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 580021 580021 580021 580021 580021 580021
## ..$ Sample : chr [1:6] "SRS5583369" "SRS5583370" "SRS5583371" "SRS5583372" ...
## ..$ BioSample : chr [1:6] "SAMN13149386" "SAMN13149385" "SAMN13149384" "SAMN13149383" ...
## ..$ 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] "SRA986231" "SRA986231" "SRA986231" "SRA986231" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "C127A1B4FCFADEC94B8C6CDB9229B834" "F9CE0CDB0DDEB35D3F3F86F375FCF5F4" "6A1BC5A7CC88A62A068B237A19EF97DE" "978192D19512BB5A0FA36A87D81DB4C4" ...
## ..$ ReadHash : chr [1:6] "1642BAE509DDA3D5269EF1EEB3A9AD70" "DB0395696BAA55B40F764A34E7F75430" "1CF7A06A453FFD8447A7344DDFAC0DE7" "DCC45C5B493B8724F64D0BF52625E19E" ...
## $ 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
## SRP227272: Calu-3 cells mock infection versus MERS-CoV 24 hours post infection (mRNA): mock;SRX7066767,SRX7066768,SRX7066769: 24 hours post infection;SRX7066773,SRX7066774,SRX7066775;## 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:
## ..$ SRR10357366: int [1:58302] 0 131 0 0 0 0 0 0 0 1 ...
## ..$ SRR10357367: int [1:58302] 0 80 0 0 0 0 0 0 0 1 ...
## ..$ SRR10357368: int [1:58302] 0 107 0 0 0 0 0 0 0 4 ...
## ..$ SRR10357372: int [1:58302] 0 74 0 0 0 0 1 0 0 2 ...
## ..$ SRR10357373: int [1:58302] 0 93 0 0 0 0 0 0 0 4 ...
## ..$ SRR10357374: int [1:58302] 0 67 0 0 0 0 0 0 0 2 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR10357366: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357367: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357368: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357372: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357373: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357374: 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:
## ..$ SRR10357366: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357367: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357368: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357372: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357373: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357374: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "FAIL(3,4,6)" ...
## ..$ SRX_accession: chr [1:6] "SRX7066767" "SRX7066768" "SRX7066769" "SRX7066773" ...
## ..$ SRS_accession: chr [1:6] "SRS5583369" "SRS5583370" "SRS5583371" "SRS5583375" ...
## ..$ SRP_accession: chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142814" "GSM4142815" "GSM4142816" "GSM4142820" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ 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" "FAIL(3,4,6)" ...
## ..$ SRX_accession : chr [1:6] "SRX7066767" "SRX7066768" "SRX7066769" "SRX7066773" ...
## ..$ SRS_accession : chr [1:6] "SRS5583369" "SRS5583370" "SRS5583371" "SRS5583375" ...
## ..$ SRP_accession : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142814" "GSM4142815" "GSM4142816" "GSM4142820" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4142814" "GSM4142815" "GSM4142816" "GSM4142820" ...
## ..$ ReleaseDate : chr [1:6] "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" ...
## ..$ LoadDate : chr [1:6] "2019-10-28 17:50:22" "2019-10-28 17:46:06" "2019-10-28 17:47:07" "2019-10-28 17:49:20" ...
## ..$ spots : int [1:6] 31885169 22368064 23108924 24800897 22895502 28001520
## ..$ bases : num [1:6] 9.57e+09 6.71e+09 6.93e+09 7.44e+09 6.87e+09 ...
## ..$ spots_with_mates : int [1:6] 31885169 22368064 23108924 24800897 22895502 28001520
## ..$ avgLength : int [1:6] 300 300 300 300 300 300
## ..$ size_MB : int [1:6] 3767 2669 2761 2857 2665 3544
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/010114/SRR10357366" "https://sra-download.ncbi.nlm.nih.gov/traces/sra30/SRR/010114/SRR10357367" "https://sra-download.ncbi.nlm.nih.gov/traces/sra29/SRR/010114/SRR10357368" "https://sra-download.ncbi.nlm.nih.gov/traces/sra27/SRR/010114/SRR10357372" ...
## ..$ 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] "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" ...
## ..$ SRAStudy : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ BioProject : chr [1:6] "PRJNA580021" "PRJNA580021" "PRJNA580021" "PRJNA580021" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 580021 580021 580021 580021 580021 580021
## ..$ Sample : chr [1:6] "SRS5583369" "SRS5583370" "SRS5583371" "SRS5583375" ...
## ..$ BioSample : chr [1:6] "SAMN13149386" "SAMN13149385" "SAMN13149384" "SAMN13149380" ...
## ..$ 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] "SRA986231" "SRA986231" "SRA986231" "SRA986231" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "C127A1B4FCFADEC94B8C6CDB9229B834" "F9CE0CDB0DDEB35D3F3F86F375FCF5F4" "6A1BC5A7CC88A62A068B237A19EF97DE" "79CFA23B8EC77513FCC8A16A90D68A70" ...
## ..$ ReadHash : chr [1:6] "1642BAE509DDA3D5269EF1EEB3A9AD70" "DB0395696BAA55B40F764A34E7F75430" "1CF7A06A453FFD8447A7344DDFAC0DE7" "949D6EAEFA25EE3A6815A8CA672F3820" ...
## $ absent : chr(0)## SRP227272: Calu-3 cells mock infection versus MERS-CoV 6 hours post infection (miRNA): mock;SRX7066776,SRX7066777,SRX7066778: 6 hours post infection;SRX7066779,SRX7066780,SRX7066781;
## 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:
## ..$ SRR10357375: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357376: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357377: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357378: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357379: int [1:58302] 1 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR10357380: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR10357375: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357376: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357377: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357378: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357379: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357380: 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:
## ..$ SRR10357375: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357376: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357377: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357378: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357379: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357380: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## $ 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] "SRX7066776" "SRX7066777" "SRX7066778" "SRX7066779" ...
## ..$ SRS_accession: chr [1:6] "SRS5583378" "SRS5583379" "SRS5583380" "SRS5583381" ...
## ..$ SRP_accession: chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142823" "GSM4142824" "GSM4142825" "GSM4142826" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ 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] "SRX7066776" "SRX7066777" "SRX7066778" "SRX7066779" ...
## ..$ SRS_accession : chr [1:6] "SRS5583378" "SRS5583379" "SRS5583380" "SRS5583381" ...
## ..$ SRP_accession : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142823" "GSM4142824" "GSM4142825" "GSM4142826" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4142823" "GSM4142824" "GSM4142825" "GSM4142826" ...
## ..$ ReleaseDate : chr [1:6] "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" ...
## ..$ LoadDate : chr [1:6] "2019-10-28 17:44:25" "2019-10-28 17:50:28" "2019-10-28 17:43:18" "2019-10-28 17:41:57" ...
## ..$ spots : int [1:6] 22791114 27930767 20754629 20561063 21286785 21507714
## ..$ bases : num [1:6] 6.84e+09 8.38e+09 6.23e+09 6.17e+09 6.39e+09 ...
## ..$ spots_with_mates : int [1:6] 22791114 27930767 20754629 20561063 21286785 21507714
## ..$ avgLength : int [1:6] 300 300 300 300 300 300
## ..$ size_MB : int [1:6] 2293 2860 2156 2080 2125 2167
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra30/SRR/010114/SRR10357375" "https://sra-download.ncbi.nlm.nih.gov/traces/sra36/SRR/010114/SRR10357376" "https://sra-download.ncbi.nlm.nih.gov/traces/sra32/SRR/010114/SRR10357377" "https://sra-download.ncbi.nlm.nih.gov/traces/sra17/SRR/010114/SRR10357378" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "miRNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "size fractionation" ...
## ..$ 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] "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" ...
## ..$ SRAStudy : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ BioProject : chr [1:6] "PRJNA580021" "PRJNA580021" "PRJNA580021" "PRJNA580021" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 580021 580021 580021 580021 580021 580021
## ..$ Sample : chr [1:6] "SRS5583378" "SRS5583379" "SRS5583380" "SRS5583381" ...
## ..$ BioSample : chr [1:6] "SAMN13149377" "SAMN13149376" "SAMN13149375" "SAMN13149374" ...
## ..$ 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] "SRA986231" "SRA986231" "SRA986231" "SRA986231" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "60856CF6273C98574657289689867FF8" "54054E469D73D700DC363791530D5555" "88D9450B3259A32DD63CE9D2FC2791C9" "988E6A803441AF2E6C56799DEB08FFE8" ...
## ..$ ReadHash : chr [1:6] "DD9C81270073F3699A650BB74F12D69C" "57F1E999179371F5E50300FD3863ACEC" "E5BD6746A7DF863AAB30A0C0B41C26D3" "92EFAAAF22FBDD5A5C0907A1A69B9006" ...
## $ absent : chr(0)## SRP227272: Calu-3 cells mock infection versus MERS-CoV 24 hours post infection (miRNA): mock;SRX7066776,SRX7066777,SRX7066778: 24 hours post infection;SRX7066782,SRX7066783,SRX7066784;
## 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:
## ..$ SRR10357375: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357376: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357377: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357381: int [1:58302] 1 1 0 0 0 0 0 1 0 0 ...
## ..$ SRR10357382: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR10357383: int [1:58302] 0 1 0 0 0 0 0 0 0 2 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR10357375: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357376: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357377: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357381: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357382: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357383: num [1:180869] 0 0 0 0 0 0 0.5 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:
## ..$ SRR10357375: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357376: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357377: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357381: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357382: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357383: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(4,6)" "FAIL(4,6)" "FAIL(4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession: chr [1:6] "SRX7066776" "SRX7066777" "SRX7066778" "SRX7066782" ...
## ..$ SRS_accession: chr [1:6] "SRS5583378" "SRS5583379" "SRS5583380" "SRS5583384" ...
## ..$ SRP_accession: chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142823" "GSM4142824" "GSM4142825" "GSM4142829" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ 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(3,4,6)" ...
## ..$ SRX_accession : chr [1:6] "SRX7066776" "SRX7066777" "SRX7066778" "SRX7066782" ...
## ..$ SRS_accession : chr [1:6] "SRS5583378" "SRS5583379" "SRS5583380" "SRS5583384" ...
## ..$ SRP_accession : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142823" "GSM4142824" "GSM4142825" "GSM4142829" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4142823" "GSM4142824" "GSM4142825" "GSM4142829" ...
## ..$ ReleaseDate : chr [1:6] "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" ...
## ..$ LoadDate : chr [1:6] "2019-10-28 17:44:25" "2019-10-28 17:50:28" "2019-10-28 17:43:18" "2019-10-28 17:47:09" ...
## ..$ spots : int [1:6] 22791114 27930767 20754629 27856225 24700170 23314353
## ..$ bases : num [1:6] 6.84e+09 8.38e+09 6.23e+09 8.36e+09 7.41e+09 ...
## ..$ spots_with_mates : int [1:6] 22791114 27930767 20754629 27856225 24700170 23314353
## ..$ avgLength : int [1:6] 300 300 300 300 300 300
## ..$ size_MB : int [1:6] 2293 2860 2156 2683 2424 2323
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra30/SRR/010114/SRR10357375" "https://sra-download.ncbi.nlm.nih.gov/traces/sra36/SRR/010114/SRR10357376" "https://sra-download.ncbi.nlm.nih.gov/traces/sra32/SRR/010114/SRR10357377" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/010114/SRR10357381" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "miRNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "size fractionation" ...
## ..$ 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] "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" ...
## ..$ SRAStudy : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ BioProject : chr [1:6] "PRJNA580021" "PRJNA580021" "PRJNA580021" "PRJNA580021" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 580021 580021 580021 580021 580021 580021
## ..$ Sample : chr [1:6] "SRS5583378" "SRS5583379" "SRS5583380" "SRS5583384" ...
## ..$ BioSample : chr [1:6] "SAMN13149377" "SAMN13149376" "SAMN13149375" "SAMN13149371" ...
## ..$ 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] "SRA986231" "SRA986231" "SRA986231" "SRA986231" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "60856CF6273C98574657289689867FF8" "54054E469D73D700DC363791530D5555" "88D9450B3259A32DD63CE9D2FC2791C9" "AE54BC8A47F3F600C4E512C693968C03" ...
## ..$ ReadHash : chr [1:6] "DD9C81270073F3699A650BB74F12D69C" "57F1E999179371F5E50300FD3863ACEC" "E5BD6746A7DF863AAB30A0C0B41C26D3" "90399CFC4EE889EC05A68A4D33D626E1" ...
## $ absent : chr(0)## SRP227272: Calu-3 cells mock infection versus MERS-CoV 6 hours post infection (cirRNA): mock;SRX7066785,SRX7066786,SRX7066787: 6 hours post infection;SRX7066788,SRX7066789,SRX7066790;
## 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:
## ..$ SRR10357384: int [1:58302] 0 7 36 0 0 0 0 0 0 1 ...
## ..$ SRR10357385: int [1:58302] 0 9 44 0 0 0 0 0 0 2 ...
## ..$ SRR10357386: int [1:58302] 0 19 47 0 0 0 0 0 0 3 ...
## ..$ SRR10357387: int [1:58302] 0 17 26 0 0 0 0 0 0 10 ...
## ..$ SRR10357388: int [1:58302] 0 36 19 0 0 0 0 0 0 4 ...
## ..$ SRR10357389: int [1:58302] 0 34 32 0 0 0 0 0 0 7 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR10357384: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357385: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357386: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357387: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357388: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357389: 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:
## ..$ SRR10357384: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357385: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357386: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357387: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357388: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357389: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession: chr [1:6] "SRX7066785" "SRX7066786" "SRX7066787" "SRX7066788" ...
## ..$ SRS_accession: chr [1:6] "SRS5583387" "SRS5583388" "SRS5583389" "SRS5583390" ...
## ..$ SRP_accession: chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142832" "GSM4142833" "GSM4142834" "GSM4142835" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ 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(3,4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession : chr [1:6] "SRX7066785" "SRX7066786" "SRX7066787" "SRX7066788" ...
## ..$ SRS_accession : chr [1:6] "SRS5583387" "SRS5583388" "SRS5583389" "SRS5583390" ...
## ..$ SRP_accession : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142832" "GSM4142833" "GSM4142834" "GSM4142835" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4142832" "GSM4142833" "GSM4142834" "GSM4142835" ...
## ..$ ReleaseDate : chr [1:6] "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" ...
## ..$ LoadDate : chr [1:6] "2019-10-28 17:54:40" "2019-10-28 18:02:48" "2019-10-28 18:07:05" "2019-10-28 18:00:59" ...
## ..$ spots : int [1:6] 41197500 50747540 63198971 48665415 35150946 52786072
## ..$ bases : num [1:6] 1.24e+10 1.52e+10 1.90e+10 1.46e+10 1.05e+10 ...
## ..$ spots_with_mates : int [1:6] 41197500 50747540 63198971 48665415 35150946 52786072
## ..$ avgLength : int [1:6] 300 300 300 300 300 300
## ..$ size_MB : int [1:6] 4656 5761 7161 5285 3202 5747
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra28/SRR/010114/SRR10357384" "https://sra-download.ncbi.nlm.nih.gov/traces/sra28/SRR/010114/SRR10357385" "https://sra-download.ncbi.nlm.nih.gov/traces/sra22/SRR/010114/SRR10357386" "https://sra-download.ncbi.nlm.nih.gov/traces/sra28/SRR/010114/SRR10357387" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "ncRNA-Seq" "ncRNA-Seq" "ncRNA-Seq" "ncRNA-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] "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] "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" ...
## ..$ SRAStudy : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ BioProject : chr [1:6] "PRJNA580021" "PRJNA580021" "PRJNA580021" "PRJNA580021" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 580021 580021 580021 580021 580021 580021
## ..$ Sample : chr [1:6] "SRS5583387" "SRS5583388" "SRS5583389" "SRS5583390" ...
## ..$ BioSample : chr [1:6] "SAMN13149368" "SAMN13149367" "SAMN13149393" "SAMN13149392" ...
## ..$ 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] "SRA986231" "SRA986231" "SRA986231" "SRA986231" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "63B2F5037CF2A4F5D8BD86FCC3925D50" "05289E53E3ABE72C1B14490378D71EAA" "00E6EDB06BFEE8C5CFED9E17E8D91ED5" "6627F700A77FB61BAD8E53DCC974BFB3" ...
## ..$ ReadHash : chr [1:6] "6E14015695A254DE42FCCFA3E04E0C5E" "5F0CB49091D4DC74376C3B4966136B7C" "F37307894EAEC0E0F3C05397EE5BAEB1" "94396360CB632C48C546F7F95D2440B2" ...
## $ absent : chr(0)## SRP227272: Calu-3 cells mock infection versus MERS-CoV 24 hours post infection (cirRNA):mock;SRX7066785,SRX7066786,SRX7066787: 24 hours post infection;SRX7066791,SRX7066792,SRX7066793;
## 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:
## ..$ SRR10357384: int [1:58302] 0 7 36 0 0 0 0 0 0 1 ...
## ..$ SRR10357385: int [1:58302] 0 9 44 0 0 0 0 0 0 2 ...
## ..$ SRR10357386: int [1:58302] 0 19 47 0 0 0 0 0 0 3 ...
## ..$ SRR10357390: int [1:58302] 0 33 6 0 0 0 0 0 0 8 ...
## ..$ SRR10357391: int [1:58302] 0 27 7 0 0 0 0 0 0 12 ...
## ..$ SRR10357392: int [1:58302] 0 15 1 0 0 0 0 0 0 4 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR10357384: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357385: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357386: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357390: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357391: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10357392: 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:
## ..$ SRR10357384: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357385: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357386: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357390: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357391: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## ..$ SRR10357392: chr [1:30] "PE" "Sanger/Illumina1.9" "150" "150" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(3,4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession: chr [1:6] "SRX7066785" "SRX7066786" "SRX7066787" "SRX7066791" ...
## ..$ SRS_accession: chr [1:6] "SRS5583387" "SRS5583388" "SRS5583389" "SRS5583393" ...
## ..$ SRP_accession: chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142832" "GSM4142833" "GSM4142834" "GSM4142838" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ 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(3,4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession : chr [1:6] "SRX7066785" "SRX7066786" "SRX7066787" "SRX7066791" ...
## ..$ SRS_accession : chr [1:6] "SRS5583387" "SRS5583388" "SRS5583389" "SRS5583393" ...
## ..$ SRP_accession : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ Sample_name : chr [1:6] "GSM4142832" "GSM4142833" "GSM4142834" "GSM4142838" ...
## ..$ GEO_series : chr [1:6] "GSE139516" "GSE139516" "GSE139516" "GSE139516" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4142832" "GSM4142833" "GSM4142834" "GSM4142838" ...
## ..$ ReleaseDate : chr [1:6] "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" "2019-12-01 21:17:11" ...
## ..$ LoadDate : chr [1:6] "2019-10-28 17:54:40" "2019-10-28 18:02:48" "2019-10-28 18:07:05" "2019-10-28 18:20:34" ...
## ..$ spots : int [1:6] 41197500 50747540 63198971 56334571 64101858 38010535
## ..$ bases : num [1:6] 1.24e+10 1.52e+10 1.90e+10 1.69e+10 1.92e+10 ...
## ..$ spots_with_mates : int [1:6] 41197500 50747540 63198971 56334571 64101858 38010535
## ..$ avgLength : int [1:6] 300 300 300 300 300 300
## ..$ size_MB : int [1:6] 4656 5761 7161 6156 6955 4159
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra28/SRR/010114/SRR10357384" "https://sra-download.ncbi.nlm.nih.gov/traces/sra28/SRR/010114/SRR10357385" "https://sra-download.ncbi.nlm.nih.gov/traces/sra22/SRR/010114/SRR10357386" "https://sra-download.ncbi.nlm.nih.gov/traces/sra30/SRR/010114/SRR10357390" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "ncRNA-Seq" "ncRNA-Seq" "ncRNA-Seq" "ncRNA-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] "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] "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" "HiSeq X Ten" ...
## ..$ SRAStudy : chr [1:6] "SRP227272" "SRP227272" "SRP227272" "SRP227272" ...
## ..$ BioProject : chr [1:6] "PRJNA580021" "PRJNA580021" "PRJNA580021" "PRJNA580021" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 580021 580021 580021 580021 580021 580021
## ..$ Sample : chr [1:6] "SRS5583387" "SRS5583388" "SRS5583389" "SRS5583393" ...
## ..$ BioSample : chr [1:6] "SAMN13149368" "SAMN13149367" "SAMN13149393" "SAMN13149389" ...
## ..$ 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] "SRA986231" "SRA986231" "SRA986231" "SRA986231" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "63B2F5037CF2A4F5D8BD86FCC3925D50" "05289E53E3ABE72C1B14490378D71EAA" "00E6EDB06BFEE8C5CFED9E17E8D91ED5" "88294C1DDF846D9958F4EB24F82AEE95" ...
## ..$ ReadHash : chr [1:6] "6E14015695A254DE42FCCFA3E04E0C5E" "5F0CB49091D4DC74376C3B4966136B7C" "F37307894EAEC0E0F3C05397EE5BAEB1" "84FAE0D9702F0FB52CB5AA16755EA743" ...
## $ absent : chr(0)lapply(data,length)## [[1]]
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## [1] 1data <- data[which(lapply(data,length)>1)]
data <- data[which(lapply(data,function(x) length(x[[5]] ))>0)]
saveRDS(data,"sarsmers_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]] )
attributes(gs)$class <- "GMT"
write.GMT(gs,"sarsmers_ensemblIDs.gmt")
gs1 <- lapply(data, function(x) { x[7] })
gs2 <- lapply(data, function(x) { x[8] })
gs <- c(gs1,gs2)
gs <- lapply(gs,function(x) x[[1]] )
gs <- lapply(gs,function(x) { x[[3]] <- unique(x[[3]] ) ; return(x) } )
attributes(gs)$class <- "GMT"
write.GMT(gs,"sarsmers_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