Heart Disease
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/heartdisease.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] 53# get the metadata now to save time
mdat <- getDEE2::getDEE2Metadata(species = SPECIES)
# lets prototype this main(x[[2]])
# now go ahead and run the whole thing
data <- lapply(x,function(x) { main(x,mdat) })## SRP224657: aortic valve stenosis versus aortic valve sclerosis: stenosis; SRX6959190, SRX6959191, SRX6959192: sclerosis; SRX6959193, SRX6959194, SRX6959195;## 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:
## ..$ SRR10240188: int [1:58302] 0 15 0 0 0 0 0 0 0 0 ...
## ..$ SRR10240189: int [1:58302] 0 40 7 0 0 0 0 0 0 0 ...
## ..$ SRR10240190: int [1:58302] 0 4 8 0 0 0 0 0 0 0 ...
## ..$ SRR10240191: int [1:58302] 0 0 1 0 0 0 0 0 0 0 ...
## ..$ SRR10240192: int [1:58302] 0 26 0 0 0 0 0 0 0 0 ...
## ..$ SRR10240193: int [1:58302] 0 37 1 0 0 4 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR10240188: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10240189: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10240190: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10240191: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10240192: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10240193: 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:
## ..$ SRR10240188: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10240189: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10240190: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10240191: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10240192: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10240193: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(4,6)" "FAIL(4,6)" "FAIL(3,4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession: chr [1:6] "SRX6959190" "SRX6959191" "SRX6959192" "SRX6959193" ...
## ..$ SRS_accession: chr [1:6] "SRS5485983" "SRS5485984" "SRS5485985" "SRS5485986" ...
## ..$ SRP_accession: chr [1:6] "SRP224657" "SRP224657" "SRP224657" "SRP224657" ...
## ..$ Sample_name : chr [1:6] "GSM4110729" "GSM4110730" "GSM4110731" "GSM4110732" ...
## ..$ GEO_series : chr [1:6] "GSE138531" "GSE138531" "GSE138531" "GSE138531" ...
## ..$ 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(3,4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession : chr [1:6] "SRX6959190" "SRX6959191" "SRX6959192" "SRX6959193" ...
## ..$ SRS_accession : chr [1:6] "SRS5485983" "SRS5485984" "SRS5485985" "SRS5485986" ...
## ..$ SRP_accession : chr [1:6] "SRP224657" "SRP224657" "SRP224657" "SRP224657" ...
## ..$ Sample_name : chr [1:6] "GSM4110729" "GSM4110730" "GSM4110731" "GSM4110732" ...
## ..$ GEO_series : chr [1:6] "GSE138531" "GSE138531" "GSE138531" "GSE138531" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM4110729" "GSM4110730" "GSM4110731" "GSM4110732" ...
## ..$ ReleaseDate : chr [1:6] "2019-10-09 16:50:10" "2019-10-09 16:50:10" "2019-10-09 16:50:10" "2019-10-09 16:50:10" ...
## ..$ LoadDate : chr [1:6] "2019-10-07 17:46:20" "2019-10-07 17:48:08" "2019-10-07 17:43:45" "2019-10-07 17:50:35" ...
## ..$ spots : int [1:6] 27286174 28816047 20808924 31277964 34191016 31420973
## ..$ bases : num [1:6] 6.82e+09 7.20e+09 5.20e+09 7.82e+09 8.55e+09 ...
## ..$ spots_with_mates : int [1:6] 27286174 28816047 20808924 31277964 34191016 31420973
## ..$ avgLength : int [1:6] 250 250 250 250 250 250
## ..$ size_MB : int [1:6] 2354 2637 1822 2848 3004 2746
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRR/010000/SRR10240188" "https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/010000/SRR10240189" "https://sra-download.ncbi.nlm.nih.gov/traces/sra51/SRR/010000/SRR10240190" "https://sra-download.ncbi.nlm.nih.gov/traces/sra26/SRR/010000/SRR10240191" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP224657" "SRP224657" "SRP224657" "SRP224657" ...
## ..$ BioProject : chr [1:6] "PRJNA576259" "PRJNA576259" "PRJNA576259" "PRJNA576259" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 576259 576259 576259 576259 576259 576259
## ..$ Sample : chr [1:6] "SRS5485983" "SRS5485984" "SRS5485985" "SRS5485986" ...
## ..$ BioSample : chr [1:6] "SAMN12984979" "SAMN12984978" "SAMN12984977" "SAMN12984976" ...
## ..$ 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] "SRA974334" "SRA974334" "SRA974334" "SRA974334" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "4B4F068B15811007EE420D8517F7E221" "EED2EF0C0284AC445D7A8F0ED959E33D" "4CE3AA96AA3638079643F9E57842E3FD" "08B854EED1C58DC5609AB159BF4491CC" ...
## ..$ ReadHash : chr [1:6] "E5A4F664930B971B99960145CAC0179E" "C55FEA28D8130F65EB6550558885442C" "A54AAE634FCFBC3D314BF346D50B988E" "5BC03A308CA56E58D9D317BF7E9FE449" ...
## $ absent : chr(0)## SRP237337: RNA sequencing of left ventricle from non-failing healthy controls versus left ventricle from peripartum cardiomyopathy (PPCM): control; SRX7354049, SRX7354050, SRX7354051, SRX7354319, SRX7354320, SRX7354321, SRX7354322, SRX7354323, SRX7354324, SRX7354325, SRX7354326, SRX7354327, SRX7354328, SRX7354329, SRX7354330, SRX7354331, SRX7354332, SRX7354333, SRX7354334, SRX7354335, SRX7354081, SRX7354086, SRX7354087, SRX7354089, SRX7354093, SRX7354094, SRX7354096, SRX7354099, SRX7354100, SRX7354102, SRX7354103, SRX7354104, SRX7354105, SRX7354107, SRX7354109, SRX7354110, SRX7354111, SRX7354112, SRX7354113, SRX7354116, SRX7354117, SRX7354119, SRX7354120, SRX7354122, SRX7354123, SRX7354124, SRX7354125, SRX7354126, SRX7354127, SRX7354129, SRX7354130, SRX7354131, SRX7354132, SRX7354134, SRX7354135, SRX7354137, SRX7354138, SRX7354139, SRX7354140, SRX7354142, SRX7354143, SRX7354144, SRX7354145, SRX7354148, SRX7354149, SRX7354156, SRX7354158, SRX7354164, SRX7354165, SRX7354170, SRX7354172, SRX7354176, SRX7354177, SRX7354178, SRX7354179, SRX7354180, SRX7354181, SRX7354182, SRX7354184, SRX7354185, SRX7354188, SRX7354189, SRX7354190, SRX7354192, SRX7354193, SRX7354194, SRX7354195, SRX7354196, SRX7354197, SRX7354199, SRX7354200, SRX7354201, SRX7354203, SRX7354204, SRX7354209, SRX7354210, SRX7354211, SRX7354213, SRX7354214, SRX7354215, SRX7354216, SRX7354217, SRX7354218, SRX7354219, SRX7354224, SRX7354226, SRX7354227, SRX7354229, SRX7354230, SRX7354231, SRX7354233, SRX7354234, SRX7354236, SRX7354237, SRX7354239, SRX7354241, SRX7354242, SRX7354243, SRX7354244, SRX7354245, SRX7354246, SRX7354247, SRX7354248, SRX7354249, SRX7354251, SRX7354255, SRX7354256, SRX7354257, SRX7354258, SRX7354259, SRX7354264, SRX7354265, SRX7354266, SRX7354267, SRX7354268, SRX7354269, SRX7354270, SRX7354271, SRX7354272, SRX7354273, SRX7354274, SRX7354279, SRX7354280, SRX7354281, SRX7354282, SRX7354283, SRX7354285, SRX7354287, SRX7354289, SRX7354290, SRX7354293, SRX7354295, SRX7354300, SRX7354303, SRX7354306, SRX7354308, SRX7354309, SRX7354311, SRX7354316, SRX7354307, SRX7354151, SRX7354084, SRX7354205, SRX7354206, SRX7354207, SRX7354208: PPCM; SRX7354336, SRX7354337, SRX7354357, SRX7354118, SRX7354146, SRX7354163;
## 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 171 variables:
## ..$ SRR10676821: int [1:58302] 0 20 2 0 0 0 0 0 0 22 ...
## ..$ SRR10676822: int [1:58302] 0 47 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676823: int [1:58302] 0 64 3 0 0 0 0 0 0 2 ...
## ..$ SRR10676824: int [1:58302] 0 20 1 0 0 1 0 0 0 2 ...
## ..$ SRR10676825: int [1:58302] 0 23 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676826: int [1:58302] 0 38 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676827: int [1:58302] 0 23 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676828: int [1:58302] 0 24 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676829: int [1:58302] 1 45 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676830: int [1:58302] 0 152 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676831: int [1:58302] 0 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676832: int [1:58302] 0 67 1 0 0 0 0 0 0 1 ...
## ..$ SRR10676833: int [1:58302] 0 11 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676834: int [1:58302] 0 27 0 0 0 2 0 0 0 0 ...
## ..$ SRR10676835: int [1:58302] 0 69 6 0 0 0 0 0 0 0 ...
## ..$ SRR10676836: int [1:58302] 0 195 11 0 0 0 0 0 0 0 ...
## ..$ SRR10676837: int [1:58302] 0 35 5 0 0 0 0 0 0 1 ...
## ..$ SRR10676838: int [1:58302] 0 216 6 2 0 0 0 0 0 5 ...
## ..$ SRR10676839: int [1:58302] 0 76 6 0 0 0 0 0 0 0 ...
## ..$ SRR10676840: int [1:58302] 1 48 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676841: int [1:58302] 0 21 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676842: int [1:58302] 0 93 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676862: int [1:58302] 0 12 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676949: int [1:58302] 0 109 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676952: int [1:58302] 0 89 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676954: int [1:58302] 0 24 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676955: int [1:58302] 0 199 16 0 0 0 0 0 0 0 ...
## ..$ SRR10676957: int [1:58302] 0 21 0 0 0 0 0 0 0 1 ...
## ..$ SRR10676961: int [1:58302] 0 24 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676962: int [1:58302] 0 33 7 0 0 0 0 0 0 2 ...
## ..$ SRR10676964: int [1:58302] 0 36 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676967: int [1:58302] 0 27 3 0 0 0 0 0 0 1 ...
## ..$ SRR10676968: int [1:58302] 0 75 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676970: int [1:58302] 0 30 3 0 0 0 0 0 0 1 ...
## ..$ SRR10676971: int [1:58302] 0 18 3 0 0 0 0 0 0 1 ...
## ..$ SRR10676972: int [1:58302] 0 56 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676973: int [1:58302] 0 14 0 0 0 0 0 0 0 1 ...
## ..$ SRR10676975: int [1:58302] 0 59 1 1 0 0 0 0 0 3 ...
## ..$ SRR10676977: int [1:58302] 0 26 3 1 0 0 0 0 0 1 ...
## ..$ SRR10676978: int [1:58302] 0 42 2 0 0 0 0 0 0 1 ...
## ..$ SRR10676979: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676980: int [1:58302] 0 26 1 0 0 0 0 0 0 1 ...
## ..$ SRR10676981: int [1:58302] 0 23 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676984: int [1:58302] 1 97 3 0 0 0 0 0 0 3 ...
## ..$ SRR10676985: int [1:58302] 0 17 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676986: int [1:58302] 0 10 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676987: int [1:58302] 0 17 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676988: int [1:58302] 0 46 1 0 0 0 0 0 0 2 ...
## ..$ SRR10676990: int [1:58302] 0 51 7 0 0 0 0 0 0 0 ...
## ..$ SRR10676991: int [1:58302] 0 60 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676992: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676993: int [1:58302] 0 43 2 0 0 0 0 0 0 3 ...
## ..$ SRR10676994: int [1:58302] 0 37 9 0 0 0 0 0 0 1 ...
## ..$ SRR10676995: int [1:58302] 0 271 2 0 0 0 0 0 0 1 ...
## ..$ SRR10676997: int [1:58302] 0 41 1 0 0 0 0 0 0 2 ...
## ..$ SRR10676998: int [1:58302] 0 18 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676999: int [1:58302] 0 39 1 0 0 0 0 0 0 0 ...
## ..$ SRR10677000: int [1:58302] 0 41 2 0 0 0 0 0 0 0 ...
## ..$ SRR10677002: int [1:58302] 0 27 1 0 0 0 0 0 0 1 ...
## ..$ SRR10677003: int [1:58302] 0 19 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677005: int [1:58302] 0 11 2 1 0 0 0 0 0 0 ...
## ..$ SRR10677006: int [1:58302] 0 275 5 0 0 0 0 0 0 0 ...
## ..$ SRR10677007: int [1:58302] 0 104 7 1 0 0 0 1 0 2 ...
## ..$ SRR10677008: int [1:58302] 0 167 19 0 0 0 0 0 0 3 ...
## ..$ SRR10677010: int [1:58302] 0 49 2 0 0 0 0 0 0 7 ...
## ..$ SRR10677011: int [1:58302] 0 28 0 1 0 0 0 0 0 0 ...
## ..$ SRR10677012: int [1:58302] 0 40 2 0 0 0 0 0 0 0 ...
## ..$ SRR10677013: int [1:58302] 0 83 3 0 0 1 0 0 0 0 ...
## ..$ SRR10677014: int [1:58302] 0 209 3 0 0 0 0 0 0 0 ...
## ..$ SRR10677016: int [1:58302] 0 8 2 0 0 0 0 0 0 0 ...
## ..$ SRR10677017: int [1:58302] 0 125 5 0 0 0 0 0 0 3 ...
## ..$ SRR10677019: int [1:58302] 0 51 1 0 0 0 0 0 0 1 ...
## ..$ SRR10677024: int [1:58302] 0 11 0 0 0 0 1 0 0 0 ...
## ..$ SRR10677026: int [1:58302] 0 22 5 0 0 0 0 0 0 0 ...
## ..$ SRR10677031: int [1:58302] 0 39 8 0 0 0 0 0 0 0 ...
## ..$ SRR10677032: int [1:58302] 0 28 5 0 0 0 0 0 0 0 ...
## ..$ SRR10677033: int [1:58302] 0 28 4 0 0 0 0 0 0 0 ...
## ..$ SRR10677038: int [1:58302] 1 9 1 0 0 0 0 0 0 0 ...
## ..$ SRR10677040: int [1:58302] 0 59 2 0 0 0 0 0 0 1 ...
## ..$ SRR10677044: int [1:58302] 1 42 3 0 0 0 0 0 0 7 ...
## ..$ SRR10677045: int [1:58302] 1 205 9 1 0 0 0 0 0 6 ...
## ..$ SRR10677046: int [1:58302] 0 44 4 0 0 0 0 0 0 1 ...
## ..$ SRR10677047: int [1:58302] 0 62 4 0 0 0 0 0 0 1 ...
## ..$ SRR10677048: int [1:58302] 0 34 3 0 0 0 0 0 0 0 ...
## ..$ SRR10677049: int [1:58302] 0 74 11 0 0 0 0 0 0 0 ...
## ..$ SRR10677050: int [1:58302] 0 27 3 0 0 0 0 0 0 1 ...
## ..$ SRR10677052: int [1:58302] 0 69 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677053: int [1:58302] 0 46 7 0 0 0 0 0 0 1 ...
## ..$ SRR10677056: int [1:58302] 0 78 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677057: int [1:58302] 0 26 1 0 0 0 0 0 0 1 ...
## ..$ SRR10677058: int [1:58302] 0 112 9 0 0 0 0 0 0 0 ...
## ..$ SRR10677060: int [1:58302] 0 42 1 0 0 0 0 0 0 0 ...
## ..$ SRR10677061: int [1:58302] 0 53 2 0 0 0 0 0 0 0 ...
## ..$ SRR10677062: int [1:58302] 0 8 1 0 0 0 0 0 0 0 ...
## ..$ SRR10677063: int [1:58302] 0 48 0 2 0 0 0 0 0 0 ...
## ..$ SRR10677064: int [1:58302] 0 39 6 0 0 0 0 0 0 0 ...
## ..$ SRR10677065: int [1:58302] 0 59 5 0 0 0 0 0 0 4 ...
## ..$ SRR10677067: int [1:58302] 0 210 0 0 0 1 0 0 0 0 ...
## ..$ SRR10677068: int [1:58302] 0 129 8 0 0 0 0 0 1 1 ...
## .. [list output truncated]
## $ TxCounts :'data.frame': 180869 obs. of 171 variables:
## ..$ SRR10676821: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676822: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676823: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676824: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676825: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676826: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676827: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676828: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676829: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676830: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676831: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676832: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676833: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676834: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676835: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676836: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676837: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676838: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676839: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676840: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676841: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676842: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676862: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676949: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676952: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676954: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676955: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676957: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676961: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676962: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676964: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676967: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676968: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676970: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676971: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676972: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676973: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676975: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676977: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676978: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676984: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676985: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676986: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676987: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676988: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676990: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676991: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676992: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676993: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676994: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676995: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676997: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676998: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676999: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677000: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677002: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677003: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677005: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677006: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677007: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677008: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677010: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677011: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677012: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677013: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677014: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677016: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677017: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677019: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677024: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677026: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677031: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677032: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677033: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677038: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677040: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677044: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677045: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677046: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677047: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677048: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677049: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677050: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677052: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677053: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677056: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677057: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677058: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677060: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677061: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677062: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677063: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677064: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677065: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677067: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677068: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## .. [list output truncated]
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 171 variables:
## ..$ SRR10676821: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676822: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676823: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676824: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676825: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676826: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676827: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676828: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676829: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676830: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676831: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676832: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676833: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676834: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676835: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676836: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676837: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676838: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676839: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676840: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676841: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676842: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676862: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676949: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676952: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676954: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676955: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676957: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676961: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676962: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676964: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676967: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676968: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676970: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676971: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676972: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676973: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676975: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676977: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676978: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676979: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676980: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676981: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676984: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676985: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676986: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676987: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676988: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676990: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676991: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676992: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676993: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676994: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676995: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676997: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676998: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676999: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677000: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677002: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677003: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677005: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677006: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677007: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677008: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677010: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677011: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677012: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677013: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677014: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677016: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677017: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677019: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677024: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677026: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677031: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677032: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677033: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677038: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677040: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677044: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677045: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677046: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677047: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677048: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677049: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677050: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677052: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677053: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677056: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677057: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677058: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677060: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677061: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677062: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677063: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677064: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677065: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677067: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677068: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## .. [list output truncated]
## $ MetadataSummary:'data.frame': 171 obs. of 7 variables:
## ..$ QC_summary : chr [1:171] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:171] "SRX7354049" "SRX7354050" "SRX7354051" "SRX7354319" ...
## ..$ SRS_accession: chr [1:171] "SRS5813426" "SRS5813427" "SRS5813428" "SRS5813696" ...
## ..$ SRP_accession: chr [1:171] "SRP237337" "SRP237337" "SRP237337" "SRP237337" ...
## ..$ Sample_name : chr [1:171] "GSM4215858" "GSM4215859" "GSM4215860" "GSM4215861" ...
## ..$ GEO_series : chr [1:171] "GSE141910" "GSE141910" "GSE141910" "GSE141910" ...
## ..$ Library_name : logi [1:171] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 171 obs. of 52 variables:
## ..$ QC_summary : chr [1:171] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:171] "SRX7354049" "SRX7354050" "SRX7354051" "SRX7354319" ...
## ..$ SRS_accession : chr [1:171] "SRS5813426" "SRS5813427" "SRS5813428" "SRS5813696" ...
## ..$ SRP_accession : chr [1:171] "SRP237337" "SRP237337" "SRP237337" "SRP237337" ...
## ..$ Sample_name : chr [1:171] "GSM4215858" "GSM4215859" "GSM4215860" "GSM4215861" ...
## ..$ GEO_series : chr [1:171] "GSE141910" "GSE141910" "GSE141910" "GSE141910" ...
## ..$ Library_name : logi [1:171] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:171] "GSM4215858" "GSM4215859" "GSM4215860" "GSM4215861" ...
## ..$ ReleaseDate : chr [1:171] "2019-12-16 19:16:13" "2019-12-16 19:16:13" "2019-12-16 19:16:13" "2019-12-16 19:16:20" ...
## ..$ LoadDate : chr [1:171] "2019-12-12 20:19:46" "2019-12-12 21:50:43" "2019-12-12 20:13:21" "2019-12-12 20:31:04" ...
## ..$ spots : int [1:171] 46626404 82369206 32838058 53886679 31851010 44271183 34334525 40100669 40054193 65629221 ...
## ..$ bases : num [1:171] 1.17e+10 2.24e+10 8.21e+09 1.35e+10 7.96e+09 ...
## ..$ spots_with_mates : int [1:171] 46626404 82369206 32838058 53886679 31851010 44271183 34334525 40100669 40054193 65629221 ...
## ..$ avgLength : int [1:171] 250 272 250 250 250 250 250 250 250 271 ...
## ..$ size_MB : int [1:171] 4182 8266 2844 4946 2693 4041 2832 3355 3644 6578 ...
## ..$ AssemblyName : logi [1:171] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:171] "https://sra-download.ncbi.nlm.nih.gov/traces/sra23/SRR/010426/SRR10676821" "https://sra-download.ncbi.nlm.nih.gov/traces/sra13/SRR/010426/SRR10676822" "https://sra-download.ncbi.nlm.nih.gov/traces/sra58/SRR/010426/SRR10676823" "https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/010426/SRR10676824" ...
## ..$ LibraryName : logi [1:171] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:171] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:171] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:171] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:171] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:171] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:171] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:171] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:171] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:171] "SRP237337" "SRP237337" "SRP237337" "SRP237337" ...
## ..$ BioProject : chr [1:171] "PRJNA595151" "PRJNA595151" "PRJNA595151" "PRJNA595151" ...
## ..$ Study_Pubmed_id : logi [1:171] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:171] 595151 595151 595151 595151 595151 595151 595151 595151 595151 595151 ...
## ..$ Sample : chr [1:171] "SRS5813426" "SRS5813427" "SRS5813428" "SRS5813696" ...
## ..$ BioSample : chr [1:171] "SAMN13546631" "SAMN13546630" "SAMN13546629" "SAMN13546628" ...
## ..$ SampleType : chr [1:171] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:171] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:171] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:171] NA NA NA NA NA NA ...
## ..$ source : logi [1:171] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:171] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:171] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:171] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:171] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:171] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:171] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:171] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:171] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:171] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:171] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:171] "SRA1011145" "SRA1011145" "SRA1011145" "SRA1011145" ...
## ..$ dbgap_study_accession: logi [1:171] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:171] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:171] "CE1C34258BA703D06FD90B4C99483A58" "B022A5A22729486253FDCB30EFF926A9" "AB596CCA579C0CA1BD38B7F84A064373" "D60F7E3FB1AE4DCF21ACD01D0A49DABA" ...
## ..$ ReadHash : chr [1:171] "266132EBC609EA94F53CCF71E4AFC071" "5B58DA0A330A2B8C91B9B5AFD87A76C2" "658DFF99235B31BAF23515A7BA5FBCA5" "0E9F5955B9FE756104AB7C516B408CC9" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 250 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP237337: RNA sequencing of left ventricle from non-failing healthy controls versus left ventricle from hypertrophic cardiomyopathy (HCM): control; SRX7354049, SRX7354050, SRX7354051, SRX7354319, SRX7354320, SRX7354321, SRX7354322, SRX7354323, SRX7354324, SRX7354325, SRX7354326, SRX7354327, SRX7354328, SRX7354329, SRX7354330, SRX7354331, SRX7354332, SRX7354333, SRX7354334, SRX7354335, SRX7354081, SRX7354086, SRX7354087, SRX7354089, SRX7354093, SRX7354094, SRX7354096, SRX7354099, SRX7354100, SRX7354102, SRX7354103, SRX7354104, SRX7354105, SRX7354107, SRX7354109, SRX7354110, SRX7354111, SRX7354112, SRX7354113, SRX7354116, SRX7354117, SRX7354119, SRX7354120, SRX7354122, SRX7354123, SRX7354124, SRX7354125, SRX7354126, SRX7354127, SRX7354129, SRX7354130, SRX7354131, SRX7354132, SRX7354134, SRX7354135, SRX7354137, SRX7354138, SRX7354139, SRX7354140, SRX7354142, SRX7354143, SRX7354144, SRX7354145, SRX7354148, SRX7354149, SRX7354156, SRX7354158, SRX7354164, SRX7354165, SRX7354170, SRX7354172, SRX7354176, SRX7354177, SRX7354178, SRX7354179, SRX7354180, SRX7354181, SRX7354182, SRX7354184, SRX7354185, SRX7354188, SRX7354189, SRX7354190, SRX7354192, SRX7354193, SRX7354194, SRX7354195, SRX7354196, SRX7354197, SRX7354199, SRX7354200, SRX7354201, SRX7354203, SRX7354204, SRX7354209, SRX7354210, SRX7354211, SRX7354213, SRX7354214, SRX7354215, SRX7354216, SRX7354217, SRX7354218, SRX7354219, SRX7354224, SRX7354226, SRX7354227, SRX7354229, SRX7354230, SRX7354231, SRX7354233, SRX7354234, SRX7354236, SRX7354237, SRX7354239, SRX7354241, SRX7354242, SRX7354243, SRX7354244, SRX7354245, SRX7354246, SRX7354247, SRX7354248, SRX7354249, SRX7354251, SRX7354255, SRX7354256, SRX7354257, SRX7354258, SRX7354259, SRX7354264, SRX7354265, SRX7354266, SRX7354267, SRX7354268, SRX7354269, SRX7354270, SRX7354271, SRX7354272, SRX7354273, SRX7354274, SRX7354279, SRX7354280, SRX7354281, SRX7354282, SRX7354283, SRX7354285, SRX7354287, SRX7354289, SRX7354290, SRX7354293, SRX7354295, SRX7354300, SRX7354303, SRX7354306, SRX7354308, SRX7354309, SRX7354311, SRX7354316, SRX7354307, SRX7354151, SRX7354084, SRX7354205, SRX7354206, SRX7354207, SRX7354208: HCM; SRX7354338, SRX7354345, SRX7354390, SRX7354399, SRX7354408, SRX7354409, SRX7354412, SRX7354053, SRX7354055, SRX7354071, SRX7354080, SRX7354133, SRX7354141, SRX7354159, SRX7354173, SRX7354174, SRX7354183, SRX7354220, SRX7354221, SRX7354228, SRX7354232, SRX7354240, SRX7354252, SRX7354254, SRX7354294, SRX7354313, SRX7354314, SRX7354202;## 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 193 variables:
## ..$ SRR10676821: int [1:58302] 0 20 2 0 0 0 0 0 0 22 ...
## ..$ SRR10676822: int [1:58302] 0 47 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676823: int [1:58302] 0 64 3 0 0 0 0 0 0 2 ...
## ..$ SRR10676824: int [1:58302] 0 20 1 0 0 1 0 0 0 2 ...
## ..$ SRR10676825: int [1:58302] 0 23 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676826: int [1:58302] 0 38 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676827: int [1:58302] 0 23 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676828: int [1:58302] 0 24 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676829: int [1:58302] 1 45 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676830: int [1:58302] 0 152 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676831: int [1:58302] 0 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676832: int [1:58302] 0 67 1 0 0 0 0 0 0 1 ...
## ..$ SRR10676833: int [1:58302] 0 11 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676834: int [1:58302] 0 27 0 0 0 2 0 0 0 0 ...
## ..$ SRR10676835: int [1:58302] 0 69 6 0 0 0 0 0 0 0 ...
## ..$ SRR10676836: int [1:58302] 0 195 11 0 0 0 0 0 0 0 ...
## ..$ SRR10676837: int [1:58302] 0 35 5 0 0 0 0 0 0 1 ...
## ..$ SRR10676838: int [1:58302] 0 216 6 2 0 0 0 0 0 5 ...
## ..$ SRR10676839: int [1:58302] 0 76 6 0 0 0 0 0 0 0 ...
## ..$ SRR10676840: int [1:58302] 1 48 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676843: int [1:58302] 0 21 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676850: int [1:58302] 0 47 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676895: int [1:58302] 0 34 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676904: int [1:58302] 0 11 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676913: int [1:58302] 0 26 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676914: int [1:58302] 0 83 12 0 0 0 0 0 0 6 ...
## ..$ SRR10676917: int [1:58302] 0 57 10 0 0 0 0 0 0 0 ...
## ..$ SRR10676921: int [1:58302] 0 33 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676923: int [1:58302] 0 73 13 0 0 0 0 1 0 4 ...
## ..$ SRR10676939: int [1:58302] 0 74 0 0 0 0 0 0 0 1 ...
## ..$ SRR10676948: int [1:58302] 0 35 6 0 0 0 0 0 0 0 ...
## ..$ SRR10676949: int [1:58302] 0 109 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676952: int [1:58302] 0 89 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676954: int [1:58302] 0 24 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676955: int [1:58302] 0 199 16 0 0 0 0 0 0 0 ...
## ..$ SRR10676957: int [1:58302] 0 21 0 0 0 0 0 0 0 1 ...
## ..$ SRR10676961: int [1:58302] 0 24 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676962: int [1:58302] 0 33 7 0 0 0 0 0 0 2 ...
## ..$ SRR10676964: int [1:58302] 0 36 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676967: int [1:58302] 0 27 3 0 0 0 0 0 0 1 ...
## ..$ SRR10676968: int [1:58302] 0 75 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676970: int [1:58302] 0 30 3 0 0 0 0 0 0 1 ...
## ..$ SRR10676971: int [1:58302] 0 18 3 0 0 0 0 0 0 1 ...
## ..$ SRR10676972: int [1:58302] 0 56 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676973: int [1:58302] 0 14 0 0 0 0 0 0 0 1 ...
## ..$ SRR10676975: int [1:58302] 0 59 1 1 0 0 0 0 0 3 ...
## ..$ SRR10676977: int [1:58302] 0 26 3 1 0 0 0 0 0 1 ...
## ..$ SRR10676978: int [1:58302] 0 42 2 0 0 0 0 0 0 1 ...
## ..$ SRR10676979: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676980: int [1:58302] 0 26 1 0 0 0 0 0 0 1 ...
## ..$ SRR10676981: int [1:58302] 0 23 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676984: int [1:58302] 1 97 3 0 0 0 0 0 0 3 ...
## ..$ SRR10676985: int [1:58302] 0 17 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676987: int [1:58302] 0 17 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676988: int [1:58302] 0 46 1 0 0 0 0 0 0 2 ...
## ..$ SRR10676990: int [1:58302] 0 51 7 0 0 0 0 0 0 0 ...
## ..$ SRR10676991: int [1:58302] 0 60 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676992: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676993: int [1:58302] 0 43 2 0 0 0 0 0 0 3 ...
## ..$ SRR10676994: int [1:58302] 0 37 9 0 0 0 0 0 0 1 ...
## ..$ SRR10676995: int [1:58302] 0 271 2 0 0 0 0 0 0 1 ...
## ..$ SRR10676997: int [1:58302] 0 41 1 0 0 0 0 0 0 2 ...
## ..$ SRR10676998: int [1:58302] 0 18 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676999: int [1:58302] 0 39 1 0 0 0 0 0 0 0 ...
## ..$ SRR10677000: int [1:58302] 0 41 2 0 0 0 0 0 0 0 ...
## ..$ SRR10677001: int [1:58302] 0 38 1 0 0 0 0 0 0 1 ...
## ..$ SRR10677002: int [1:58302] 0 27 1 0 0 0 0 0 0 1 ...
## ..$ SRR10677003: int [1:58302] 0 19 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677005: int [1:58302] 0 11 2 1 0 0 0 0 0 0 ...
## ..$ SRR10677006: int [1:58302] 0 275 5 0 0 0 0 0 0 0 ...
## ..$ SRR10677007: int [1:58302] 0 104 7 1 0 0 0 1 0 2 ...
## ..$ SRR10677008: int [1:58302] 0 167 19 0 0 0 0 0 0 3 ...
## ..$ SRR10677009: int [1:58302] 0 40 3 0 0 0 0 0 0 1 ...
## ..$ SRR10677010: int [1:58302] 0 49 2 0 0 0 0 0 0 7 ...
## ..$ SRR10677011: int [1:58302] 0 28 0 1 0 0 0 0 0 0 ...
## ..$ SRR10677012: int [1:58302] 0 40 2 0 0 0 0 0 0 0 ...
## ..$ SRR10677013: int [1:58302] 0 83 3 0 0 1 0 0 0 0 ...
## ..$ SRR10677016: int [1:58302] 0 8 2 0 0 0 0 0 0 0 ...
## ..$ SRR10677017: int [1:58302] 0 125 5 0 0 0 0 0 0 3 ...
## ..$ SRR10677019: int [1:58302] 0 51 1 0 0 0 0 0 0 1 ...
## ..$ SRR10677024: int [1:58302] 0 11 0 0 0 0 1 0 0 0 ...
## ..$ SRR10677026: int [1:58302] 0 22 5 0 0 0 0 0 0 0 ...
## ..$ SRR10677027: int [1:58302] 0 110 1 0 0 0 0 0 0 0 ...
## ..$ SRR10677032: int [1:58302] 0 28 5 0 0 0 0 0 0 0 ...
## ..$ SRR10677033: int [1:58302] 0 28 4 0 0 0 0 0 0 0 ...
## ..$ SRR10677038: int [1:58302] 1 9 1 0 0 0 0 0 0 0 ...
## ..$ SRR10677040: int [1:58302] 0 59 2 0 0 0 0 0 0 1 ...
## ..$ SRR10677041: int [1:58302] 1 52 3 0 0 0 0 0 0 0 ...
## ..$ SRR10677042: int [1:58302] 0 16 1 1 0 0 0 0 0 0 ...
## ..$ SRR10677044: int [1:58302] 1 42 3 0 0 0 0 0 0 7 ...
## ..$ SRR10677045: int [1:58302] 1 205 9 1 0 0 0 0 0 6 ...
## ..$ SRR10677046: int [1:58302] 0 44 4 0 0 0 0 0 0 1 ...
## ..$ SRR10677047: int [1:58302] 0 62 4 0 0 0 0 0 0 1 ...
## ..$ SRR10677048: int [1:58302] 0 34 3 0 0 0 0 0 0 0 ...
## ..$ SRR10677049: int [1:58302] 0 74 11 0 0 0 0 0 0 0 ...
## ..$ SRR10677050: int [1:58302] 0 27 3 0 0 0 0 0 0 1 ...
## ..$ SRR10677051: int [1:58302] 0 82 11 0 0 0 0 0 0 0 ...
## ..$ SRR10677052: int [1:58302] 0 69 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677053: int [1:58302] 0 46 7 0 0 0 0 0 0 1 ...
## .. [list output truncated]
## $ TxCounts :'data.frame': 180869 obs. of 193 variables:
## ..$ SRR10676821: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676822: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676823: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676824: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676825: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676826: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676827: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676828: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676829: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676830: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676831: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676832: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676833: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676834: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676835: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676836: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676837: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676838: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676839: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676840: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676843: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676850: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676895: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676904: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676913: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676914: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676917: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676921: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676923: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676939: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676948: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676949: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676952: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676954: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676955: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676957: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676961: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676962: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676964: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676967: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676968: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676970: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676971: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676972: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676973: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676975: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676977: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676978: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676984: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676985: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676987: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676988: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676990: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676991: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676992: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676993: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676994: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676995: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676997: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676998: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676999: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677000: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677001: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677002: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677003: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677005: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677006: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677007: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677008: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677009: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677010: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677011: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677012: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677013: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677016: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677017: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677019: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677024: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677026: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677027: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677032: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677033: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677038: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677040: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677041: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677042: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677044: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677045: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677046: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677047: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677048: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677049: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677050: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677051: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677052: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10677053: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## .. [list output truncated]
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 193 variables:
## ..$ SRR10676821: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676822: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676823: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676824: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676825: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676826: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676827: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676828: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676829: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676830: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676831: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676832: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676833: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676834: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676835: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676836: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676837: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676838: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676839: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676840: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676843: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676850: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676895: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676904: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676913: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676914: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676917: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676921: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676923: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676939: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676948: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676949: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676952: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676954: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676955: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676957: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676961: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676962: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676964: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676967: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676968: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676970: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676971: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676972: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676973: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676975: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676977: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676978: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676979: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676980: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676981: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676984: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676985: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676987: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676988: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676990: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676991: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676992: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676993: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676994: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676995: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676997: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676998: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676999: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677000: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677001: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677002: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677003: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677005: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677006: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677007: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677008: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677009: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677010: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677011: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677012: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677013: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677016: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677017: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677019: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677024: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677026: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677027: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677032: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677033: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677038: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677040: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677041: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677042: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677044: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677045: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677046: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677047: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677048: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677049: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677050: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677051: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677052: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10677053: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## .. [list output truncated]
## $ MetadataSummary:'data.frame': 193 obs. of 7 variables:
## ..$ QC_summary : chr [1:193] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:193] "SRX7354049" "SRX7354050" "SRX7354051" "SRX7354319" ...
## ..$ SRS_accession: chr [1:193] "SRS5813426" "SRS5813427" "SRS5813428" "SRS5813696" ...
## ..$ SRP_accession: chr [1:193] "SRP237337" "SRP237337" "SRP237337" "SRP237337" ...
## ..$ Sample_name : chr [1:193] "GSM4215858" "GSM4215859" "GSM4215860" "GSM4215861" ...
## ..$ GEO_series : chr [1:193] "GSE141910" "GSE141910" "GSE141910" "GSE141910" ...
## ..$ Library_name : logi [1:193] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 193 obs. of 52 variables:
## ..$ QC_summary : chr [1:193] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:193] "SRX7354049" "SRX7354050" "SRX7354051" "SRX7354319" ...
## ..$ SRS_accession : chr [1:193] "SRS5813426" "SRS5813427" "SRS5813428" "SRS5813696" ...
## ..$ SRP_accession : chr [1:193] "SRP237337" "SRP237337" "SRP237337" "SRP237337" ...
## ..$ Sample_name : chr [1:193] "GSM4215858" "GSM4215859" "GSM4215860" "GSM4215861" ...
## ..$ GEO_series : chr [1:193] "GSE141910" "GSE141910" "GSE141910" "GSE141910" ...
## ..$ Library_name : logi [1:193] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:193] "GSM4215858" "GSM4215859" "GSM4215860" "GSM4215861" ...
## ..$ ReleaseDate : chr [1:193] "2019-12-16 19:16:13" "2019-12-16 19:16:13" "2019-12-16 19:16:13" "2019-12-16 19:16:20" ...
## ..$ LoadDate : chr [1:193] "2019-12-12 20:19:46" "2019-12-12 21:50:43" "2019-12-12 20:13:21" "2019-12-12 20:31:04" ...
## ..$ spots : int [1:193] 46626404 82369206 32838058 53886679 31851010 44271183 34334525 40100669 40054193 65629221 ...
## ..$ bases : num [1:193] 1.17e+10 2.24e+10 8.21e+09 1.35e+10 7.96e+09 ...
## ..$ spots_with_mates : int [1:193] 46626404 82369206 32838058 53886679 31851010 44271183 34334525 40100669 40054193 65629221 ...
## ..$ avgLength : int [1:193] 250 272 250 250 250 250 250 250 250 271 ...
## ..$ size_MB : int [1:193] 4182 8266 2844 4946 2693 4041 2832 3355 3644 6578 ...
## ..$ AssemblyName : logi [1:193] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:193] "https://sra-download.ncbi.nlm.nih.gov/traces/sra23/SRR/010426/SRR10676821" "https://sra-download.ncbi.nlm.nih.gov/traces/sra13/SRR/010426/SRR10676822" "https://sra-download.ncbi.nlm.nih.gov/traces/sra58/SRR/010426/SRR10676823" "https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/010426/SRR10676824" ...
## ..$ LibraryName : logi [1:193] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:193] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:193] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:193] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:193] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:193] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:193] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:193] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:193] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:193] "SRP237337" "SRP237337" "SRP237337" "SRP237337" ...
## ..$ BioProject : chr [1:193] "PRJNA595151" "PRJNA595151" "PRJNA595151" "PRJNA595151" ...
## ..$ Study_Pubmed_id : logi [1:193] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:193] 595151 595151 595151 595151 595151 595151 595151 595151 595151 595151 ...
## ..$ Sample : chr [1:193] "SRS5813426" "SRS5813427" "SRS5813428" "SRS5813696" ...
## ..$ BioSample : chr [1:193] "SAMN13546631" "SAMN13546630" "SAMN13546629" "SAMN13546628" ...
## ..$ SampleType : chr [1:193] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:193] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:193] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:193] NA NA NA NA NA NA ...
## ..$ source : logi [1:193] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:193] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:193] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:193] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:193] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:193] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:193] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:193] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:193] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:193] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:193] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:193] "SRA1011145" "SRA1011145" "SRA1011145" "SRA1011145" ...
## ..$ dbgap_study_accession: logi [1:193] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:193] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:193] "CE1C34258BA703D06FD90B4C99483A58" "B022A5A22729486253FDCB30EFF926A9" "AB596CCA579C0CA1BD38B7F84A064373" "D60F7E3FB1AE4DCF21ACD01D0A49DABA" ...
## ..$ ReadHash : chr [1:193] "266132EBC609EA94F53CCF71E4AFC071" "5B58DA0A330A2B8C91B9B5AFD87A76C2" "658DFF99235B31BAF23515A7BA5FBCA5" "0E9F5955B9FE756104AB7C516B408CC9" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 153 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP237337: RNA sequencing of left ventricle from non-failing healthy controls versus left ventricle from dilated cardiomyopathy (DCM): control; SRX7354049, SRX7354050, SRX7354051, SRX7354319, SRX7354320, SRX7354321, SRX7354322, SRX7354323, SRX7354324, SRX7354325, SRX7354326, SRX7354327, SRX7354328, SRX7354329, SRX7354330, SRX7354331, SRX7354332, SRX7354333, SRX7354334, SRX7354335, SRX7354081, SRX7354086, SRX7354087, SRX7354089, SRX7354093, SRX7354094, SRX7354096, SRX7354099, SRX7354100, SRX7354102, SRX7354103, SRX7354104, SRX7354105, SRX7354107, SRX7354109, SRX7354110, SRX7354111, SRX7354112, SRX7354113, SRX7354116, SRX7354117, SRX7354119, SRX7354120, SRX7354122, SRX7354123, SRX7354124, SRX7354125, SRX7354126, SRX7354127, SRX7354129, SRX7354130, SRX7354131, SRX7354132, SRX7354134, SRX7354135, SRX7354137, SRX7354138, SRX7354139, SRX7354140, SRX7354142, SRX7354143, SRX7354144, SRX7354145, SRX7354148, SRX7354149, SRX7354156, SRX7354158, SRX7354164, SRX7354165, SRX7354170, SRX7354172, SRX7354176, SRX7354177, SRX7354178, SRX7354179, SRX7354180, SRX7354181, SRX7354182, SRX7354184, SRX7354185, SRX7354188, SRX7354189, SRX7354190, SRX7354192, SRX7354193, SRX7354194, SRX7354195, SRX7354196, SRX7354197, SRX7354199, SRX7354200, SRX7354201, SRX7354203, SRX7354204, SRX7354209, SRX7354210, SRX7354211, SRX7354213, SRX7354214, SRX7354215, SRX7354216, SRX7354217, SRX7354218, SRX7354219, SRX7354224, SRX7354226, SRX7354227, SRX7354229, SRX7354230, SRX7354231, SRX7354233, SRX7354234, SRX7354236, SRX7354237, SRX7354239, SRX7354241, SRX7354242, SRX7354243, SRX7354244, SRX7354245, SRX7354246, SRX7354247, SRX7354248, SRX7354249, SRX7354251, SRX7354255, SRX7354256, SRX7354257, SRX7354258, SRX7354259, SRX7354264, SRX7354265, SRX7354266, SRX7354267, SRX7354268, SRX7354269, SRX7354270, SRX7354271, SRX7354272, SRX7354273, SRX7354274, SRX7354279, SRX7354280, SRX7354281, SRX7354282, SRX7354283, SRX7354285, SRX7354287, SRX7354289, SRX7354290, SRX7354293, SRX7354295, SRX7354300, SRX7354303, SRX7354306, SRX7354308, SRX7354309, SRX7354311, SRX7354316, SRX7354307, SRX7354151, SRX7354084, SRX7354205, SRX7354206, SRX7354207, SRX7354208: DCM; SRX7354339, SRX7354340, SRX7354341, SRX7354342, SRX7354343, SRX7354344, SRX7354346, SRX7354347, SRX7354348, SRX7354349, SRX7354350, SRX7354351, SRX7354352, SRX7354353, SRX7354354, SRX7354355, SRX7354358, SRX7354359, SRX7354360, SRX7354361, SRX7354363, SRX7354364, SRX7354365, SRX7354366, SRX7354367, SRX7354368, SRX7354369, SRX7354370, SRX7354371, SRX7354372, SRX7354373, SRX7354374, SRX7354375, SRX7354376, SRX7354377, SRX7354378, SRX7354379, SRX7354380, SRX7354381, SRX7354382, SRX7354383, SRX7354384, SRX7354385, SRX7354386, SRX7354387, SRX7354388, SRX7354389, SRX7354391, SRX7354392, SRX7354393, SRX7354394, SRX7354395, SRX7354396, SRX7354397, SRX7354398, SRX7354400, SRX7354401, SRX7354402, SRX7354403, SRX7354404, SRX7354405, SRX7354406, SRX7354407, SRX7354410, SRX7354411, SRX7354413, SRX7354414, SRX7354052, SRX7354054, SRX7354056, SRX7354057, SRX7354058, SRX7354059, SRX7354060, SRX7354061, SRX7354062, SRX7354063, SRX7354064, SRX7354065, SRX7354066, SRX7354067, SRX7354068, SRX7354069, SRX7354070, SRX7354072, SRX7354073, SRX7354074, SRX7354075, SRX7354076, SRX7354077, SRX7354078, SRX7354079, SRX7354082, SRX7354083, SRX7354085, SRX7354088, SRX7354090, SRX7354091, SRX7354092, SRX7354095, SRX7354097, SRX7354098, SRX7354101, SRX7354106, SRX7354108, SRX7354114, SRX7354115, SRX7354121, SRX7354128, SRX7354136, SRX7354147, SRX7354150, SRX7354152, SRX7354153, SRX7354155, SRX7354157, SRX7354160, SRX7354161, SRX7354162, SRX7354167, SRX7354168, SRX7354169, SRX7354171, SRX7354175, SRX7354186, SRX7354187, SRX7354191, SRX7354198, SRX7354212, SRX7354222, SRX7354223, SRX7354235, SRX7354238, SRX7354250, SRX7354253, SRX7354260, SRX7354261, SRX7354262, SRX7354263, SRX7354275, SRX7354276, SRX7354277, SRX7354278, SRX7354284, SRX7354286, SRX7354288, SRX7354291, SRX7354292, SRX7354296, SRX7354297, SRX7354298, SRX7354299, SRX7354301, SRX7354302, SRX7354304, SRX7354305, SRX7354310, SRX7354312, SRX7354315, SRX7354317, SRX7354318, SRX7354166, SRX7354356, SRX7354362, SRX7354225, SRX7354154;## 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 330 variables:
## ..$ SRR10676821: int [1:58302] 0 20 2 0 0 0 0 0 0 22 ...
## ..$ SRR10676822: int [1:58302] 0 47 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676823: int [1:58302] 0 64 3 0 0 0 0 0 0 2 ...
## ..$ SRR10676824: int [1:58302] 0 20 1 0 0 1 0 0 0 2 ...
## ..$ SRR10676825: int [1:58302] 0 23 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676826: int [1:58302] 0 38 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676827: int [1:58302] 0 23 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676828: int [1:58302] 0 24 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676829: int [1:58302] 1 45 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676830: int [1:58302] 0 152 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676831: int [1:58302] 0 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676832: int [1:58302] 0 67 1 0 0 0 0 0 0 1 ...
## ..$ SRR10676833: int [1:58302] 0 11 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676834: int [1:58302] 0 27 0 0 0 2 0 0 0 0 ...
## ..$ SRR10676835: int [1:58302] 0 69 6 0 0 0 0 0 0 0 ...
## ..$ SRR10676836: int [1:58302] 0 195 11 0 0 0 0 0 0 0 ...
## ..$ SRR10676837: int [1:58302] 0 35 5 0 0 0 0 0 0 1 ...
## ..$ SRR10676838: int [1:58302] 0 216 6 2 0 0 0 0 0 5 ...
## ..$ SRR10676839: int [1:58302] 0 76 6 0 0 0 0 0 0 0 ...
## ..$ SRR10676840: int [1:58302] 1 48 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676844: int [1:58302] 0 25 0 1 0 0 0 0 0 0 ...
## ..$ SRR10676845: int [1:58302] 0 32 2 1 0 0 0 0 0 0 ...
## ..$ SRR10676846: int [1:58302] 0 15 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676847: int [1:58302] 0 25 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676848: int [1:58302] 0 104 10 0 0 0 0 0 0 0 ...
## ..$ SRR10676849: int [1:58302] 0 82 2 1 0 1 0 0 0 0 ...
## ..$ SRR10676851: int [1:58302] 0 110 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676852: int [1:58302] 0 116 4 3 0 0 0 0 0 1 ...
## ..$ SRR10676853: int [1:58302] 0 34 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676854: int [1:58302] 0 32 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676855: int [1:58302] 0 22 3 0 0 0 0 0 0 1 ...
## ..$ SRR10676856: int [1:58302] 0 28 0 1 0 0 0 0 0 2 ...
## ..$ SRR10676857: int [1:58302] 0 87 8 1 0 0 0 0 0 1 ...
## ..$ SRR10676858: int [1:58302] 0 36 9 0 0 0 0 0 0 1 ...
## ..$ SRR10676859: int [1:58302] 0 21 5 0 0 0 0 1 0 0 ...
## ..$ SRR10676860: int [1:58302] 0 15 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676861: int [1:58302] 0 10 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676863: int [1:58302] 0 29 7 3 0 0 0 0 0 0 ...
## ..$ SRR10676864: int [1:58302] 0 58 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676865: int [1:58302] 0 33 7 0 0 0 0 0 0 0 ...
## ..$ SRR10676866: int [1:58302] 0 22 2 1 0 0 0 0 0 0 ...
## ..$ SRR10676867: int [1:58302] 0 90 1 0 0 0 0 0 0 7 ...
## ..$ SRR10676868: int [1:58302] 0 27 1 0 0 0 0 0 0 3 ...
## ..$ SRR10676869: int [1:58302] 0 32 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676870: int [1:58302] 0 6 0 0 0 0 0 0 0 1 ...
## ..$ SRR10676871: int [1:58302] 0 47 0 2 0 0 0 0 0 0 ...
## ..$ SRR10676872: int [1:58302] 0 11 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676873: int [1:58302] 0 38 3 0 0 0 0 0 0 1 ...
## ..$ SRR10676874: int [1:58302] 0 26 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676875: int [1:58302] 0 25 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676876: int [1:58302] 0 44 14 0 0 0 0 0 0 1 ...
## ..$ SRR10676877: int [1:58302] 0 24 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676878: int [1:58302] 0 88 7 0 0 0 0 0 0 0 ...
## ..$ SRR10676879: int [1:58302] 0 24 1 0 0 0 0 0 0 1 ...
## ..$ SRR10676880: int [1:58302] 0 74 7 0 0 0 0 0 0 1 ...
## ..$ SRR10676881: int [1:58302] 0 28 3 1 0 0 0 0 0 0 ...
## ..$ SRR10676882: int [1:58302] 0 22 8 0 0 0 0 0 0 7 ...
## ..$ SRR10676883: int [1:58302] 0 24 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676884: int [1:58302] 0 182 11 0 0 0 0 0 0 0 ...
## ..$ SRR10676885: int [1:58302] 0 17 2 0 0 1 0 0 0 0 ...
## ..$ SRR10676886: int [1:58302] 0 19 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676887: int [1:58302] 0 89 12 0 0 0 0 0 0 0 ...
## ..$ SRR10676888: int [1:58302] 0 56 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676889: int [1:58302] 0 27 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676890: int [1:58302] 0 37 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676891: int [1:58302] 0 42 7 0 0 0 0 0 0 2 ...
## ..$ SRR10676892: int [1:58302] 0 20 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676893: int [1:58302] 0 42 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676894: int [1:58302] 0 259 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676896: int [1:58302] 0 16 3 1 0 0 0 0 0 0 ...
## ..$ SRR10676897: int [1:58302] 0 50 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676898: int [1:58302] 0 146 20 0 0 0 0 0 0 1 ...
## ..$ SRR10676899: int [1:58302] 0 62 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676900: int [1:58302] 0 18 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676901: int [1:58302] 0 34 6 0 0 0 0 0 0 0 ...
## ..$ SRR10676902: int [1:58302] 0 289 34 0 0 0 0 0 0 1 ...
## ..$ SRR10676903: int [1:58302] 0 38 5 0 0 0 0 0 0 0 ...
## ..$ SRR10676905: int [1:58302] 0 127 13 0 0 0 0 0 0 0 ...
## ..$ SRR10676906: int [1:58302] 0 16 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676907: int [1:58302] 0 18 2 0 0 0 0 0 0 1 ...
## ..$ SRR10676908: int [1:58302] 0 30 3 0 0 0 0 0 0 0 ...
## ..$ SRR10676910: int [1:58302] 0 44 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676911: int [1:58302] 0 21 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676912: int [1:58302] 0 47 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676915: int [1:58302] 0 22 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676916: int [1:58302] 0 22 2 0 0 0 0 0 0 1 ...
## ..$ SRR10676918: int [1:58302] 0 33 4 0 0 1 0 0 0 0 ...
## ..$ SRR10676919: int [1:58302] 0 282 3 3 0 0 0 0 0 0 ...
## ..$ SRR10676920: int [1:58302] 0 41 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676922: int [1:58302] 0 43 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676924: int [1:58302] 0 28 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676925: int [1:58302] 0 49 4 0 0 0 0 0 0 0 ...
## ..$ SRR10676926: int [1:58302] 0 51 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676927: int [1:58302] 0 40 2 0 0 0 0 0 0 2 ...
## ..$ SRR10676928: int [1:58302] 1 28 2 1 0 0 0 0 0 0 ...
## ..$ SRR10676929: int [1:58302] 0 78 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676930: int [1:58302] 0 17 1 0 0 0 0 0 0 0 ...
## ..$ SRR10676931: int [1:58302] 0 190 2 0 0 0 0 0 0 0 ...
## ..$ SRR10676932: int [1:58302] 0 130 5 0 0 0 0 0 0 0 ...
## .. [list output truncated]
## $ TxCounts :'data.frame': 180869 obs. of 330 variables:
## ..$ SRR10676821: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676822: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676823: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676824: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676825: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676826: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676827: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676828: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676829: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676830: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676831: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676832: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676833: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676834: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676835: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676836: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676837: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676838: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676839: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676840: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676844: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676845: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676846: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676847: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676848: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676849: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676851: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676852: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676853: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676854: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676855: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676856: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676857: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676858: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676859: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676860: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676861: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676863: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676864: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676865: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676866: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676867: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676868: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676869: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676870: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676871: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676872: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676873: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676874: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676875: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676876: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676877: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676878: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676879: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676880: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676881: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676882: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676883: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676884: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676885: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676886: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676887: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676888: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676889: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676890: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676891: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676892: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676893: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676894: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676896: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676897: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676898: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676899: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676900: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676901: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676902: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676903: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676905: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676906: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676907: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676908: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676910: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676911: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676912: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676915: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676916: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676918: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676919: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676920: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676922: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676924: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676925: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676926: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676927: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676928: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676929: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676930: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676931: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10676932: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## .. [list output truncated]
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 330 variables:
## ..$ SRR10676821: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676822: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676823: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676824: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676825: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676826: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676827: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676828: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676829: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676830: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676831: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676832: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676833: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676834: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676835: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676836: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676837: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676838: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676839: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676840: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676844: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676845: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676846: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676847: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676848: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676849: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676851: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676852: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676853: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676854: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676855: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676856: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676857: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676858: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676859: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676860: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676861: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676863: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676864: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676865: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676866: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676867: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676868: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676869: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676870: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676871: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676872: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676873: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676874: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676875: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676876: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676877: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676878: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676879: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676880: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676881: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676882: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676883: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676884: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676885: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676886: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676887: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676888: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676889: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676890: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676891: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676892: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676893: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676894: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676896: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676897: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676898: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676899: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676900: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676901: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676902: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676903: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676905: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676906: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676907: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676908: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676910: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676911: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676912: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676915: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676916: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676918: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676919: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676920: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676922: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676924: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676925: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676926: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676927: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676928: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676929: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676930: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676931: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## ..$ SRR10676932: chr [1:30] "PE" "Sanger/Illumina1.9" "125" "125" ...
## .. [list output truncated]
## $ MetadataSummary:'data.frame': 330 obs. of 7 variables:
## ..$ QC_summary : chr [1:330] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:330] "SRX7354049" "SRX7354050" "SRX7354051" "SRX7354319" ...
## ..$ SRS_accession: chr [1:330] "SRS5813426" "SRS5813427" "SRS5813428" "SRS5813696" ...
## ..$ SRP_accession: chr [1:330] "SRP237337" "SRP237337" "SRP237337" "SRP237337" ...
## ..$ Sample_name : chr [1:330] "GSM4215858" "GSM4215859" "GSM4215860" "GSM4215861" ...
## ..$ GEO_series : chr [1:330] "GSE141910" "GSE141910" "GSE141910" "GSE141910" ...
## ..$ Library_name : logi [1:330] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 330 obs. of 52 variables:
## ..$ QC_summary : chr [1:330] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:330] "SRX7354049" "SRX7354050" "SRX7354051" "SRX7354319" ...
## ..$ SRS_accession : chr [1:330] "SRS5813426" "SRS5813427" "SRS5813428" "SRS5813696" ...
## ..$ SRP_accession : chr [1:330] "SRP237337" "SRP237337" "SRP237337" "SRP237337" ...
## ..$ Sample_name : chr [1:330] "GSM4215858" "GSM4215859" "GSM4215860" "GSM4215861" ...
## ..$ GEO_series : chr [1:330] "GSE141910" "GSE141910" "GSE141910" "GSE141910" ...
## ..$ Library_name : logi [1:330] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:330] "GSM4215858" "GSM4215859" "GSM4215860" "GSM4215861" ...
## ..$ ReleaseDate : chr [1:330] "2019-12-16 19:16:13" "2019-12-16 19:16:13" "2019-12-16 19:16:13" "2019-12-16 19:16:20" ...
## ..$ LoadDate : chr [1:330] "2019-12-12 20:19:46" "2019-12-12 21:50:43" "2019-12-12 20:13:21" "2019-12-12 20:31:04" ...
## ..$ spots : int [1:330] 46626404 82369206 32838058 53886679 31851010 44271183 34334525 40100669 40054193 65629221 ...
## ..$ bases : num [1:330] 1.17e+10 2.24e+10 8.21e+09 1.35e+10 7.96e+09 ...
## ..$ spots_with_mates : int [1:330] 46626404 82369206 32838058 53886679 31851010 44271183 34334525 40100669 40054193 65629221 ...
## ..$ avgLength : int [1:330] 250 272 250 250 250 250 250 250 250 271 ...
## ..$ size_MB : int [1:330] 4182 8266 2844 4946 2693 4041 2832 3355 3644 6578 ...
## ..$ AssemblyName : logi [1:330] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:330] "https://sra-download.ncbi.nlm.nih.gov/traces/sra23/SRR/010426/SRR10676821" "https://sra-download.ncbi.nlm.nih.gov/traces/sra13/SRR/010426/SRR10676822" "https://sra-download.ncbi.nlm.nih.gov/traces/sra58/SRR/010426/SRR10676823" "https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/010426/SRR10676824" ...
## ..$ LibraryName : logi [1:330] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:330] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:330] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:330] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:330] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:330] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:330] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:330] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:330] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:330] "SRP237337" "SRP237337" "SRP237337" "SRP237337" ...
## ..$ BioProject : chr [1:330] "PRJNA595151" "PRJNA595151" "PRJNA595151" "PRJNA595151" ...
## ..$ Study_Pubmed_id : logi [1:330] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:330] 595151 595151 595151 595151 595151 595151 595151 595151 595151 595151 ...
## ..$ Sample : chr [1:330] "SRS5813426" "SRS5813427" "SRS5813428" "SRS5813696" ...
## ..$ BioSample : chr [1:330] "SAMN13546631" "SAMN13546630" "SAMN13546629" "SAMN13546628" ...
## ..$ SampleType : chr [1:330] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:330] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:330] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:330] NA NA NA NA NA NA ...
## ..$ source : logi [1:330] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:330] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:330] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:330] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:330] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:330] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:330] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:330] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:330] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:330] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:330] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:330] "SRA1011145" "SRA1011145" "SRA1011145" "SRA1011145" ...
## ..$ dbgap_study_accession: logi [1:330] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:330] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:330] "CE1C34258BA703D06FD90B4C99483A58" "B022A5A22729486253FDCB30EFF926A9" "AB596CCA579C0CA1BD38B7F84A064373" "D60F7E3FB1AE4DCF21ACD01D0A49DABA" ...
## ..$ ReadHash : chr [1:330] "266132EBC609EA94F53CCF71E4AFC071" "5B58DA0A330A2B8C91B9B5AFD87A76C2" "658DFF99235B31BAF23515A7BA5FBCA5" "0E9F5955B9FE756104AB7C516B408CC9" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 331 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP239802: RNA-SEQ of HUVECS (human umbilical vein endothelial cells) in full-(FM) versus differentiation medium (DM): FM; SRX7513703, SRX7513704, SRX7513705, SRX7513706: DM; SRX7513699, SRX7513700, SRX7513701, SRX7513702;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR10842892: int [1:58302] 0 1 5 0 0 0 0 0 0 0 ...
## ..$ SRR10842893: int [1:58302] 0 3 6 0 0 0 0 0 0 0 ...
## ..$ SRR10842894: int [1:58302] 0 3 3 0 0 0 0 0 0 0 ...
## ..$ SRR10842895: int [1:58302] 0 1 6 0 0 0 0 0 0 0 ...
## ..$ SRR10842896: int [1:58302] 0 4 2 0 0 0 0 0 0 0 ...
## ..$ SRR10842897: int [1:58302] 0 1 4 0 0 0 0 0 0 0 ...
## ..$ SRR10842898: int [1:58302] 0 1 4 0 0 0 0 0 0 0 ...
## ..$ SRR10842899: int [1:58302] 0 3 11 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR10842892: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10842893: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10842894: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10842895: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10842896: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10842897: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10842898: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR10842899: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR10842892: chr [1:30] "SE" "Sanger/Illumina1.9" "45" "75" ...
## ..$ SRR10842893: chr [1:30] "SE" "Sanger/Illumina1.9" "42" "75" ...
## ..$ SRR10842894: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "75" ...
## ..$ SRR10842895: chr [1:30] "SE" "Sanger/Illumina1.9" "41" "75" ...
## ..$ SRR10842896: chr [1:30] "SE" "Sanger/Illumina1.9" "59" "75" ...
## ..$ SRR10842897: chr [1:30] "SE" "Sanger/Illumina1.9" "44" "75" ...
## ..$ SRR10842898: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "75" ...
## ..$ SRR10842899: chr [1:30] "SE" "Sanger/Illumina1.9" "39" "75" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "WARN(8)" "WARN(8)" "WARN(4,8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:8] "SRX7513699" "SRX7513700" "SRX7513701" "SRX7513702" ...
## ..$ SRS_accession: chr [1:8] "SRS5953423" "SRS5953424" "SRS5953425" "SRS5953426" ...
## ..$ SRP_accession: chr [1:8] "SRP239802" "SRP239802" "SRP239802" "SRP239802" ...
## ..$ Sample_name : chr [1:8] "GSM4254146" "GSM4254147" "GSM4254148" "GSM4254149" ...
## ..$ GEO_series : chr [1:8] "GSE143148" "GSE143148" "GSE143148" "GSE143148" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "WARN(8)" "WARN(8)" "WARN(4,8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:8] "SRX7513699" "SRX7513700" "SRX7513701" "SRX7513702" ...
## ..$ SRS_accession : chr [1:8] "SRS5953423" "SRS5953424" "SRS5953425" "SRS5953426" ...
## ..$ SRP_accession : chr [1:8] "SRP239802" "SRP239802" "SRP239802" "SRP239802" ...
## ..$ Sample_name : chr [1:8] "GSM4254146" "GSM4254147" "GSM4254148" "GSM4254149" ...
## ..$ GEO_series : chr [1:8] "GSE143148" "GSE143148" "GSE143148" "GSE143148" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM4254146" "GSM4254147" "GSM4254148" "GSM4254149" ...
## ..$ ReleaseDate : chr [1:8] "2020-01-08 16:18:20" "2020-01-08 16:18:20" "2020-01-08 16:18:20" "2020-01-08 16:18:20" ...
## ..$ LoadDate : chr [1:8] "2020-01-07 13:22:25" "2020-01-07 13:19:11" "2020-01-07 13:25:30" "2020-01-07 13:20:32" ...
## ..$ spots : int [1:8] 46580771 46808077 42368422 42982697 40437274 42454625 43593482 46799890
## ..$ bases : num [1:8] 3.47e+09 3.49e+09 3.16e+09 3.20e+09 3.01e+09 ...
## ..$ spots_with_mates : int [1:8] 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:8] 74 74 74 74 74 74 74 74
## ..$ size_MB : int [1:8] 1411 1425 1285 1317 1236 1290 1325 1425
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-download.ncbi.nlm.nih.gov/traces/sra7/SRR/010588/SRR10842892" "https://sra-download.ncbi.nlm.nih.gov/traces/sra74/SRR/010588/SRR10842893" "https://sra-download.ncbi.nlm.nih.gov/traces/sra45/SRR/010588/SRR10842894" "https://sra-download.ncbi.nlm.nih.gov/traces/sra1/SRR/010588/SRR10842895" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:8] "SRP239802" "SRP239802" "SRP239802" "SRP239802" ...
## ..$ BioProject : chr [1:8] "PRJNA599372" "PRJNA599372" "PRJNA599372" "PRJNA599372" ...
## ..$ Study_Pubmed_id : int [1:8] 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:8] 599372 599372 599372 599372 599372 599372 599372 599372
## ..$ Sample : chr [1:8] "SRS5953423" "SRS5953424" "SRS5953425" "SRS5953426" ...
## ..$ BioSample : chr [1:8] "SAMN13746730" "SAMN13746728" "SAMN13746726" "SAMN13746725" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA1021367" "SRA1021367" "SRA1021367" "SRA1021367" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "4E9E641CC2E535871F2F047B0AB5C247" "B2392F0AB9BC8AA766CFE470DD3137CE" "528462B628B29CA9096F93F96CFBFDEC" "D276959555D42A349219A249628727B3" ...
## ..$ ReadHash : chr [1:8] "993E32B14927B17FD8D76835DAE019A1" "6CE7ED9629DBAFD19EF9B6F45D67BAD7" "3A1EA30D3169CC2B2264A5074086BF20" "A139936B6451ED2C310EDA9523FF71C2" ...
## $ 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
## SRP039338: non-calcified tricuspid valve versus calcified tricuspid valve: non-calcified; SRX480424, SRX480425, SRX480426, SRX480427, SRX480428, SRX480429, SRX480430, SRX480431, SRX480432, SRX480433: calcified; SRX480415, SRX480416, SRX480417, SRX480418, SRX480419, SRX480420, SRX480421, SRX480422, SRX480423;## 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 19 variables:
## ..$ SRR1181601: int [1:58302] 1 12 1 0 0 0 0 0 0 0 ...
## ..$ SRR1181602: int [1:58302] 0 20 0 1 0 0 0 0 0 1 ...
## ..$ SRR1181603: int [1:58302] 0 32 2 0 0 0 0 0 0 0 ...
## ..$ SRR1181604: int [1:58302] 0 32 0 0 0 0 0 0 0 1 ...
## ..$ SRR1181605: int [1:58302] 0 20 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181606: int [1:58302] 1 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181607: int [1:58302] 0 76 2 0 0 0 0 0 0 0 ...
## ..$ SRR1181608: int [1:58302] 0 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181609: int [1:58302] 0 39 1 2 0 0 0 0 0 0 ...
## ..$ SRR1181610: int [1:58302] 0 16 1 0 0 0 0 0 0 0 ...
## ..$ SRR1181611: int [1:58302] 0 20 0 0 0 0 0 0 0 1 ...
## ..$ SRR1181612: int [1:58302] 1 43 0 4 0 1 0 0 0 0 ...
## ..$ SRR1181613: int [1:58302] 0 19 0 1 0 0 0 0 0 2 ...
## ..$ SRR1181614: int [1:58302] 0 10 1 0 0 0 0 0 0 0 ...
## ..$ SRR1181615: int [1:58302] 0 19 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181616: int [1:58302] 0 18 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181617: int [1:58302] 0 54 2 0 0 0 0 0 0 2 ...
## ..$ SRR1181618: int [1:58302] 0 67 3 0 0 0 0 0 0 0 ...
## ..$ SRR1181619: int [1:58302] 0 14 2 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 19 variables:
## ..$ SRR1181601: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181602: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181603: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181604: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181605: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181606: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181607: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181608: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181609: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181610: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181611: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181612: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181613: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181614: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181615: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181616: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181617: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181618: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1181619: 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 19 variables:
## ..$ SRR1181601: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181602: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181603: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181604: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181605: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181606: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181607: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181608: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181609: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181610: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181611: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181612: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181613: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181614: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181615: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181616: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181617: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181618: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR1181619: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 19 obs. of 7 variables:
## ..$ QC_summary : chr [1:19] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:19] "SRX480415" "SRX480416" "SRX480417" "SRX480418" ...
## ..$ SRS_accession: chr [1:19] "SRS565353" "SRS565354" "SRS565355" "SRS565356" ...
## ..$ SRP_accession: chr [1:19] "SRP039338" "SRP039338" "SRP039338" "SRP039338" ...
## ..$ Sample_name : chr [1:19] "GSM1338124" "GSM1338125" "GSM1338126" "GSM1338127" ...
## ..$ GEO_series : chr [1:19] "GSE55492" "GSE55492" "GSE55492" "GSE55492" ...
## ..$ Library_name : logi [1:19] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 19 obs. of 52 variables:
## ..$ QC_summary : chr [1:19] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:19] "SRX480415" "SRX480416" "SRX480417" "SRX480418" ...
## ..$ SRS_accession : chr [1:19] "SRS565353" "SRS565354" "SRS565355" "SRS565356" ...
## ..$ SRP_accession : chr [1:19] "SRP039338" "SRP039338" "SRP039338" "SRP039338" ...
## ..$ Sample_name : chr [1:19] "GSM1338124" "GSM1338125" "GSM1338126" "GSM1338127" ...
## ..$ GEO_series : chr [1:19] "GSE55492" "GSE55492" "GSE55492" "GSE55492" ...
## ..$ Library_name : logi [1:19] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:19] "GSM1338124" "GSM1338125" "GSM1338126" "GSM1338127" ...
## ..$ ReleaseDate : chr [1:19] "2015-12-09 15:45:06" "2015-12-09 15:45:06" "2015-12-09 15:45:06" "2015-12-09 15:45:06" ...
## ..$ LoadDate : chr [1:19] "2016-11-15 20:20:53" "2016-11-15 20:21:01" "2016-11-15 20:24:25" "2016-11-15 20:17:08" ...
## ..$ spots : int [1:19] 16845663 19240224 26961878 21514202 9053393 9337387 25679508 7723693 39990128 19041490 ...
## ..$ bases : num [1:19] 1.51e+09 1.71e+09 2.40e+09 1.94e+09 8.14e+08 ...
## ..$ spots_with_mates : int [1:19] 13269572 14980613 21006961 17274160 7234261 7180921 19305089 5133852 29928520 14711658 ...
## ..$ avgLength : int [1:19] 89 88 88 90 89 88 87 83 87 88 ...
## ..$ size_MB : int [1:19] 660 750 1205 854 354 361 1143 290 1612 743 ...
## ..$ AssemblyName : chr [1:19] "GCA_000001405.13" "GCA_000001405.13" "GCA_000001405.13" "GCA_000001405.13" ...
## ..$ download_path : chr [1:19] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR1181601/SRR1181601.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR1181602/SRR1181602.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR1181603/SRR1181603.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR1181604/SRR1181604.2" ...
## ..$ LibraryName : logi [1:19] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:19] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:19] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:19] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:19] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:19] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:19] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:19] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:19] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:19] "SRP039338" "SRP039338" "SRP039338" "SRP039338" ...
## ..$ BioProject : chr [1:19] "PRJNA239776" "PRJNA239776" "PRJNA239776" "PRJNA239776" ...
## ..$ Study_Pubmed_id : int [1:19] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:19] 239776 239776 239776 239776 239776 239776 239776 239776 239776 239776 ...
## ..$ Sample : chr [1:19] "SRS565353" "SRS565354" "SRS565355" "SRS565356" ...
## ..$ BioSample : chr [1:19] "SAMN02670928" "SAMN02670923" "SAMN02670917" "SAMN02670915" ...
## ..$ SampleType : chr [1:19] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:19] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:19] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:19] NA NA NA NA NA NA ...
## ..$ source : logi [1:19] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:19] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:19] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:19] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:19] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:19] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:19] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:19] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:19] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:19] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:19] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:19] "SRA143578" "SRA143578" "SRA143578" "SRA143578" ...
## ..$ dbgap_study_accession: logi [1:19] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:19] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:19] "C00EC5AC5D51DD4AE5A843B1BF783DF4" "436762F83273805485E3C7B3466545D6" "D1DD6152E4ECBD8BEFA4A1994090CD23" "BDB6CC05FAEC722B1188354E2E4171D6" ...
## ..$ ReadHash : chr [1:19] "579ECF024F63E3D66E9FE6DD9E911C31" "225D328C54F13511BED3C6F968BB0439" "12DF036FBFBCDC295E4879B6AEF2E3B5" "4DD5FA8CCCA748B8594EB317FF017B60" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 149 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP045420: human induced pluripotent stem cell-derived control cardiomyocytes versus human induced pluripotent stem cell-derived ET-1 (endothelin 1) stimulated cardiomyocytes: control; SRX674306, SRX674308, SRX674310: ET-1 stimulated; SRX674307, SRX674309, SRX6743011;## 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:
## ..$ SRR1542714: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1542715: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1542716: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1542717: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1542718: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR1542714: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1542715: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1542716: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1542717: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1542718: 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:
## ..$ SRR1542714: chr [1:30] "SE" "Sanger/Illumina1.9" "8" "22" ...
## ..$ SRR1542715: chr [1:30] "SE" "Sanger/Illumina1.9" "8" "22" ...
## ..$ SRR1542716: chr [1:30] "SE" "Sanger/Illumina1.9" "8" "22" ...
## ..$ SRR1542717: chr [1:30] "SE" "Sanger/Illumina1.9" "8" "22" ...
## ..$ SRR1542718: chr [1:30] "SE" "Sanger/Illumina1.9" "10" "22" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "FAIL(3,4,5,6,7)" "FAIL(4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(1,3,4,5,6,7)" ...
## ..$ SRX_accession: chr [1:5] "SRX674306" "SRX674307" "SRX674308" "SRX674309" ...
## ..$ SRS_accession: chr [1:5] "SRS678003" "SRS678004" "SRS678007" "SRS678005" ...
## ..$ SRP_accession: chr [1:5] "SRP045420" "SRP045420" "SRP045420" "SRP045420" ...
## ..$ Sample_name : chr [1:5] "GSM1470353" "GSM1470354" "GSM1470355" "GSM1470356" ...
## ..$ GEO_series : chr [1:5] "GSE60292" "GSE60292" "GSE60292" "GSE60292" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "FAIL(3,4,5,6,7)" "FAIL(4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(1,3,4,5,6,7)" ...
## ..$ SRX_accession : chr [1:5] "SRX674306" "SRX674307" "SRX674308" "SRX674309" ...
## ..$ SRS_accession : chr [1:5] "SRS678003" "SRS678004" "SRS678007" "SRS678005" ...
## ..$ SRP_accession : chr [1:5] "SRP045420" "SRP045420" "SRP045420" "SRP045420" ...
## ..$ Sample_name : chr [1:5] "GSM1470353" "GSM1470354" "GSM1470355" "GSM1470356" ...
## ..$ GEO_series : chr [1:5] "GSE60292" "GSE60292" "GSE60292" "GSE60292" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM1470353" "GSM1470354" "GSM1470355" "GSM1470356" ...
## ..$ ReleaseDate : chr [1:5] "2014-10-03 16:23:15" "2014-10-03 16:23:15" "2014-10-03 16:23:15" "2014-10-03 16:23:15" ...
## ..$ LoadDate : chr [1:5] "2014-08-11 09:29:35" "2014-08-11 09:29:38" "2014-08-11 09:29:42" "2014-08-11 09:29:40" ...
## ..$ spots : int [1:5] 1866654 1842228 2777542 1324705 3085962
## ..$ bases : int [1:5] 38872235 37125864 56795965 26475932 64498069
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 20 20 20 19 20
## ..$ size_MB : int [1:5] 32 30 49 23 51
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1542714/SRR1542714.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1542715/SRR1542715.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1542716/SRR1542716.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1542717/SRR1542717.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ 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] "ION_TORRENT" "ION_TORRENT" "ION_TORRENT" "ION_TORRENT" ...
## ..$ Model : chr [1:5] "Ion Torrent PGM" "Ion Torrent PGM" "Ion Torrent PGM" "Ion Torrent PGM" ...
## ..$ SRAStudy : chr [1:5] "SRP045420" "SRP045420" "SRP045420" "SRP045420" ...
## ..$ BioProject : chr [1:5] "PRJNA257970" "PRJNA257970" "PRJNA257970" "PRJNA257970" ...
## ..$ Study_Pubmed_id : int [1:5] 2 2 2 2 2
## ..$ ProjectID : int [1:5] 257970 257970 257970 257970 257970
## ..$ Sample : chr [1:5] "SRS678003" "SRS678004" "SRS678007" "SRS678005" ...
## ..$ BioSample : chr [1:5] "SAMN02980998" "SAMN02980999" "SAMN02981000" "SAMN02981001" ...
## ..$ 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] "SRA178671" "SRA178671" "SRA178671" "SRA178671" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "65F97D01D8114B062C1318D0B1B32458" "193BC07FBCC6601CCB34CCBA31ADF319" "73E8ED1DBE29E05F96341047D876058C" "906AF64D169222DFB0525B6497E6239F" ...
## ..$ ReadHash : chr [1:5] "EEEDD9585F0FBCE60033694670D7A615" "7F6419B784A06BC1A6D88D5BF4AF05B6" "1FB66BA6E47D869C22FE59BBA6004007" "7D83C681669D5681ACC471B7DE7EC8C7" ...
## $ absent : chr(0)## SRP052978: control vs dilated cardiomyopathy diagnosed patients who had undergone heart transplant: control; SRX860719, SRX860720, SRX860721, SRX860722: dilated cardiomyopathy; SRX860723, SRX860724, SRX860725, SRX860726, SRX860727, SRX860728;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR1781562: int [1:58302] 0 21 3 0 0 0 0 0 0 0 ...
## ..$ SRR1781563: int [1:58302] 0 9 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781564: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781565: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781566: int [1:58302] 0 25 3 0 0 1 0 0 0 0 ...
## ..$ SRR1781567: int [1:58302] 0 37 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781568: int [1:58302] 0 32 1 0 0 0 0 0 0 0 ...
## ..$ SRR1781569: int [1:58302] 0 28 5 1 0 0 0 0 0 0 ...
## ..$ SRR1781570: int [1:58302] 0 11 2 0 0 0 0 0 0 0 ...
## ..$ SRR1781571: int [1:58302] 1 50 2 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR1781562: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781563: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781564: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781565: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781566: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781567: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781568: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781569: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781570: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1781571: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR1781562: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1781563: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1781564: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1781565: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1781566: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1781567: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1781568: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1781569: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1781570: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1781571: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX860719" "SRX860720" "SRX860721" "SRX860722" ...
## ..$ SRS_accession: chr [1:10] "SRS832296" "SRS832294" "SRS832295" "SRS832299" ...
## ..$ SRP_accession: chr [1:10] "SRP052978" "SRP052978" "SRP052978" "SRP052978" ...
## ..$ Sample_name : chr [1:10] "GSM1597909" "GSM1597910" "GSM1597911" "GSM1597912" ...
## ..$ GEO_series : chr [1:10] "GSE65446" "GSE65446" "GSE65446" "GSE65446" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX860719" "SRX860720" "SRX860721" "SRX860722" ...
## ..$ SRS_accession : chr [1:10] "SRS832296" "SRS832294" "SRS832295" "SRS832299" ...
## ..$ SRP_accession : chr [1:10] "SRP052978" "SRP052978" "SRP052978" "SRP052978" ...
## ..$ Sample_name : chr [1:10] "GSM1597909" "GSM1597910" "GSM1597911" "GSM1597912" ...
## ..$ GEO_series : chr [1:10] "GSE65446" "GSE65446" "GSE65446" "GSE65446" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM1597909" "GSM1597910" "GSM1597911" "GSM1597912" ...
## ..$ ReleaseDate : chr [1:10] "2015-02-04 02:45:34" "2015-02-04 02:45:34" "2015-02-04 02:45:34" "2015-02-04 02:45:34" ...
## ..$ LoadDate : chr [1:10] "2015-02-03 15:21:44" "2015-02-03 15:17:20" "2015-02-03 15:20:48" "2015-02-03 15:25:28" ...
## ..$ spots : int [1:10] 74879899 51926034 58046423 75213034 65790750 43647720 54445923 53628914 53411184 57854649
## ..$ bases : num [1:10] 1.12e+10 7.79e+09 8.71e+09 1.13e+10 9.87e+09 ...
## ..$ spots_with_mates : int [1:10] 74879899 51926034 58046423 75213034 65790750 43647720 54445923 53628914 53411184 57854649
## ..$ avgLength : int [1:10] 150 150 150 150 150 150 150 150 150 150
## ..$ size_MB : int [1:10] 7479 5233 6074 7968 6477 4432 5563 5356 5381 5857
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1781562/SRR1781562.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1781563/SRR1781563.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1781564/SRR1781564.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1781565/SRR1781565.1" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" "Illumina Genome Analyzer IIx" ...
## ..$ SRAStudy : chr [1:10] "SRP052978" "SRP052978" "SRP052978" "SRP052978" ...
## ..$ BioProject : chr [1:10] "PRJNA274028" "PRJNA274028" "PRJNA274028" "PRJNA274028" ...
## ..$ Study_Pubmed_id : int [1:10] 2 2 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:10] 274028 274028 274028 274028 274028 274028 274028 274028 274028 274028
## ..$ Sample : chr [1:10] "SRS832296" "SRS832294" "SRS832295" "SRS832299" ...
## ..$ BioSample : chr [1:10] "SAMN03320107" "SAMN03320110" "SAMN03320108" "SAMN03320111" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA235831" "SRA235831" "SRA235831" "SRA235831" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "892401E4D35D1717105552D91134EDED" "4C98E52F7818B53DB17BD542FD6933E3" "E08E8D1F897CA3703AC455804A007399" "8F674D2885D1FC4257ACBF2804F3167E" ...
## ..$ ReadHash : chr [1:10] "142E9CCEC310ACD2236474B074BB45A3" "702A6710699A389440D2CE5E54E8659F" "1A599FA543A864C05D14D2BA0608BE74" "3F797EA91A23E5D3DCF0F6425C390A04" ...
## $ 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
## SRP053296: non myocardial infarction control versus patients with non-ST-segment elevation myocardial infarction (non-STEMI): control; SRX868371, SRX868372: non-STEMI; SRX868339, SRX868340, SRX868341, SRX868342, SRX868345, SRX868346, SRX868347, SRX868348, SRX868349, SRX868350, SRX868351, SRX868352, SRX868354, SRX868356, SRX868357, SRX868359;## 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 18 variables:
## ..$ SRR1792677: int [1:58302] 73 6 0 0 0 0 0 0 0 2 ...
## ..$ SRR1792678: int [1:58302] 7 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792679: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792680: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792683: int [1:58302] 16 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792684: int [1:58302] 0 15 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792685: int [1:58302] 15 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792686: int [1:58302] 67 1 0 0 0 0 0 0 0 2 ...
## ..$ SRR1792687: int [1:58302] 2 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792688: int [1:58302] 39 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR1792689: int [1:58302] 17 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792690: int [1:58302] 2 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792692: int [1:58302] 7 37 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792694: int [1:58302] 10 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR1792695: int [1:58302] 26 10 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792697: int [1:58302] 24 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792709: int [1:58302] 5 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR1792710: int [1:58302] 224 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 18 variables:
## ..$ SRR1792677: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792678: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792679: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792680: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792683: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792684: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792685: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792686: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792687: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792688: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792689: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792690: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792692: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792694: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792695: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792697: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792709: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792710: 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 18 variables:
## ..$ SRR1792677: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792678: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792679: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792680: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792683: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792684: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792685: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792686: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792687: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792688: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792689: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792690: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792692: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792694: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792695: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792697: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792709: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792710: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## $ MetadataSummary:'data.frame': 18 obs. of 7 variables:
## ..$ QC_summary : chr [1:18] "WARN(6,8)" "WARN(6,8)" "WARN(6,8)" "WARN(6,8)" ...
## ..$ SRX_accession: chr [1:18] "SRX868339" "SRX868340" "SRX868341" "SRX868342" ...
## ..$ SRS_accession: chr [1:18] "SRS839234" "SRS839233" "SRS839232" "SRS839230" ...
## ..$ SRP_accession: chr [1:18] "SRP053296" "SRP053296" "SRP053296" "SRP053296" ...
## ..$ Sample_name : chr [1:18] "GSM1603316" "GSM1603317" "GSM1603318" "GSM1603319" ...
## ..$ GEO_series : chr [1:18] "GSE65705" "GSE65705" "GSE65705" "GSE65705" ...
## ..$ Library_name : logi [1:18] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 18 obs. of 52 variables:
## ..$ QC_summary : chr [1:18] "WARN(6,8)" "WARN(6,8)" "WARN(6,8)" "WARN(6,8)" ...
## ..$ SRX_accession : chr [1:18] "SRX868339" "SRX868340" "SRX868341" "SRX868342" ...
## ..$ SRS_accession : chr [1:18] "SRS839234" "SRS839233" "SRS839232" "SRS839230" ...
## ..$ SRP_accession : chr [1:18] "SRP053296" "SRP053296" "SRP053296" "SRP053296" ...
## ..$ Sample_name : chr [1:18] "GSM1603316" "GSM1603317" "GSM1603318" "GSM1603319" ...
## ..$ GEO_series : chr [1:18] "GSE65705" "GSE65705" "GSE65705" "GSE65705" ...
## ..$ Library_name : logi [1:18] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:18] "GSM1603316" "GSM1603317" "GSM1603318" "GSM1603319" ...
## ..$ ReleaseDate : chr [1:18] "2015-09-15 16:10:16" "2015-09-15 16:10:16" "2015-09-15 16:10:16" "2015-09-15 16:10:16" ...
## ..$ LoadDate : chr [1:18] "2019-03-08 17:19:40" "2015-02-06 12:46:08" "2015-02-06 12:05:31" "2015-02-06 12:02:36" ...
## ..$ spots : int [1:18] 100550061 142776812 59081658 55026871 93440864 92788586 79781395 68062166 75554882 70679699 ...
## ..$ bases : num [1:18] 1.51e+10 2.14e+10 8.86e+09 8.25e+09 1.40e+10 ...
## ..$ spots_with_mates : int [1:18] 100550061 0 59081658 0 93440864 0 0 0 75554882 0 ...
## ..$ avgLength : int [1:18] 150 150 150 150 150 150 150 150 150 150 ...
## ..$ size_MB : int [1:18] 6757 10078 3864 3388 6667 6231 5417 4150 4664 4917 ...
## ..$ AssemblyName : chr [1:18] "GCA_000001405.13" "GCA_000001405.13" "GCA_000001405.13" "GCA_000001405.13" ...
## ..$ download_path : chr [1:18] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792677/SRR1792677.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792678/SRR1792678.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792679/SRR1792679.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792680/SRR1792680.1" ...
## ..$ LibraryName : logi [1:18] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:18] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:18] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:18] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:18] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:18] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:18] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:18] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:18] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:18] "SRP053296" "SRP053296" "SRP053296" "SRP053296" ...
## ..$ BioProject : chr [1:18] "PRJNA274751" "PRJNA274751" "PRJNA274751" "PRJNA274751" ...
## ..$ Study_Pubmed_id : int [1:18] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:18] 274751 274751 274751 274751 274751 274751 274751 274751 274751 274751 ...
## ..$ Sample : chr [1:18] "SRS839234" "SRS839233" "SRS839232" "SRS839230" ...
## ..$ BioSample : chr [1:18] "SAMN03332119" "SAMN03332120" "SAMN03332116" "SAMN03332117" ...
## ..$ SampleType : chr [1:18] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:18] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:18] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:18] NA NA NA NA NA NA ...
## ..$ source : logi [1:18] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:18] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:18] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:18] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:18] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:18] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:18] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:18] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:18] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:18] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:18] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:18] "SRA236686" "SRA236686" "SRA236686" "SRA236686" ...
## ..$ dbgap_study_accession: logi [1:18] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:18] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:18] "BDB1C3EA589E6B570460A1E372F858DF" "815CFF927C2EC57287E6F3CF468AA5C2" "D6BC9E147B4F4ACCFABD99FCFEA1564A" "A279A2B8FC7934E08195076164D81F84" ...
## ..$ ReadHash : chr [1:18] "B2CBB048F149271949652A315428A214" "D69FCB42C282A8252D8531DA2134AC23" "E86708739640DBBB27ED0A005CA6BE3D" "BDF82850B30238D789A1B5CA0EF9588D" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 2546 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP053296: non myocardial infarction control versus patients with ST-segment elevation myocardial infarction (STEMI): control; SRX868371, SRX868372: STEMI; SRX868343, SRX868344, SRX868353, SRX868355, SRX868358, SRX868360, SRX868361, SRX868362, SRX868363, SRX868364, SRX868365, SRX868366, SRX868367, SRX868368, SRX868369, SRX868370;## 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:
## ..$ SRR1792681: int [1:58302] 8 8 0 0 0 0 0 0 0 1 ...
## ..$ SRR1792682: int [1:58302] 10 21 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792691: int [1:58302] 25 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792693: int [1:58302] 0 68 30 0 0 0 0 0 0 3 ...
## ..$ SRR1792696: int [1:58302] 6 24 0 0 0 0 0 0 0 5 ...
## ..$ SRR1792698: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792699: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792700: int [1:58302] 11 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792701: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792702: int [1:58302] 180 0 0 0 0 0 0 5 0 0 ...
## ..$ SRR1792703: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792704: int [1:58302] 17 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792705: int [1:58302] 7 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792706: int [1:58302] 18 18 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792707: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792708: int [1:58302] 50 8 0 0 0 0 0 0 0 4 ...
## ..$ SRR1792709: int [1:58302] 5 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR1792710: int [1:58302] 224 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR2981913: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR2981929: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 20 variables:
## ..$ SRR1792681: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792682: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792691: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792693: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792696: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792698: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792699: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792700: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792701: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792702: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792703: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792704: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792705: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792706: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792707: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792708: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792709: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792710: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR2981913: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR2981929: 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:
## ..$ SRR1792681: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792682: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792691: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792693: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792696: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792698: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792699: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792700: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792701: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792702: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792703: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792704: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792705: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792706: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792707: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792708: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792709: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792710: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR2981913: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR2981929: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## $ MetadataSummary:'data.frame': 20 obs. of 7 variables:
## ..$ QC_summary : chr [1:20] "WARN(6,8)" "WARN(8)" "WARN(6,8)" "WARN(6,8)" ...
## ..$ SRX_accession: chr [1:20] "SRX868343" "SRX868344" "SRX868353" "SRX868355" ...
## ..$ SRS_accession: chr [1:20] "SRS839229" "SRS839231" "SRS839220" "SRS839218" ...
## ..$ SRP_accession: chr [1:20] "SRP053296" "SRP053296" "SRP053296" "SRP053296" ...
## ..$ Sample_name : chr [1:20] "GSM1603320" "GSM1603321" "GSM1603330" "GSM1603332" ...
## ..$ GEO_series : chr [1:20] "GSE65705" "GSE65705" "GSE65705" "GSE65705" ...
## ..$ 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(6,8)" "WARN(8)" "WARN(6,8)" "WARN(6,8)" ...
## ..$ SRX_accession : chr [1:20] "SRX868343" "SRX868344" "SRX868353" "SRX868355" ...
## ..$ SRS_accession : chr [1:20] "SRS839229" "SRS839231" "SRS839220" "SRS839218" ...
## ..$ SRP_accession : chr [1:20] "SRP053296" "SRP053296" "SRP053296" "SRP053296" ...
## ..$ Sample_name : chr [1:20] "GSM1603320" "GSM1603321" "GSM1603330" "GSM1603332" ...
## ..$ GEO_series : chr [1:20] "GSE65705" "GSE65705" "GSE65705" "GSE65705" ...
## ..$ Library_name : logi [1:20] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:20] "GSM1603320" "GSM1603321" "GSM1603330" "GSM1603332" ...
## ..$ ReleaseDate : chr [1:20] "2015-09-15 16:10:16" "2015-09-15 16:10:16" "2015-09-15 16:10:16" "2015-09-15 16:10:16" ...
## ..$ LoadDate : chr [1:20] "2015-02-06 12:30:59" "2015-02-06 12:14:36" "2015-02-06 12:03:13" "2015-02-06 12:21:14" ...
## ..$ spots : int [1:20] 91839016 78463990 69361783 87334452 106889976 105918965 91364927 76436861 64431299 92702744 ...
## ..$ bases : num [1:20] 1.38e+10 1.18e+10 1.04e+10 1.31e+10 1.60e+10 ...
## ..$ spots_with_mates : int [1:20] 0 0 69361783 0 0 105918965 91364927 0 0 0 ...
## ..$ avgLength : int [1:20] 150 150 150 150 150 150 150 150 150 150 ...
## ..$ size_MB : int [1:20] 6583 5428 4837 5044 7365 6295 6002 4845 3985 6280 ...
## ..$ AssemblyName : chr [1:20] "GCA_000001405.13" "GCA_000001405.13" "GCA_000001405.13" "GCA_000001405.13" ...
## ..$ download_path : chr [1:20] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792681/SRR1792681.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792682/SRR1792682.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792691/SRR1792691.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792693/SRR1792693.1" ...
## ..$ LibraryName : logi [1:20] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:20] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:20] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:20] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:20] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:20] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:20] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:20] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:20] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:20] "SRP053296" "SRP053296" "SRP053296" "SRP053296" ...
## ..$ BioProject : chr [1:20] "PRJNA274751" "PRJNA274751" "PRJNA274751" "PRJNA274751" ...
## ..$ Study_Pubmed_id : int [1:20] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:20] 274751 274751 274751 274751 274751 274751 274751 274751 274751 274751 ...
## ..$ Sample : chr [1:20] "SRS839229" "SRS839231" "SRS839220" "SRS839218" ...
## ..$ BioSample : chr [1:20] "SAMN03332114" "SAMN03332113" "SAMN03332137" "SAMN03332121" ...
## ..$ 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] "SRA236686" "SRA236686" "SRA236686" "SRA236686" ...
## ..$ dbgap_study_accession: logi [1:20] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:20] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:20] "77256B5D65D3840E15CC807C74EBA160" "8403590CE3C924C896767B32AAB24474" "71DB9463586AB0CAAB9A56DFB67BF10E" "E45178F2270F409B540B516E0D666BC9" ...
## ..$ ReadHash : chr [1:20] "3DA5EDDF12F9A437A9DA7BBB063EF75A" "0F84B2A5E7570A764F92393E621C96F2" "270B0931C0FF5CB77603A23423A1CD24" "BB35CC3844CF5B2E1C367906842E7801" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 2122 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP053296: patients with non-ST-segment elevation myocardial infarction (non-STEMI) versus ST-segment elevation myocardial infarction (STEMI): non-STEMI; SRX868339, SRX868340, SRX868341, SRX868342, SRX868345, SRX868346, SRX868347, SRX868348, SRX868349, SRX868350, SRX868351, SRX868352, SRX868354, SRX868356, SRX868357, SRX868359: STEMI; SRX868343, SRX868344, SRX868353, SRX868355, SRX868358, SRX868360, SRX868361, SRX868362, SRX868363, SRX868364, SRX868365, SRX868366, SRX868367, SRX868368, SRX868369, SRX868370;## 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 34 variables:
## ..$ SRR1792677: int [1:58302] 73 6 0 0 0 0 0 0 0 2 ...
## ..$ SRR1792678: int [1:58302] 7 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792679: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792680: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792681: int [1:58302] 8 8 0 0 0 0 0 0 0 1 ...
## ..$ SRR1792682: int [1:58302] 10 21 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792683: int [1:58302] 16 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792684: int [1:58302] 0 15 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792685: int [1:58302] 15 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792686: int [1:58302] 67 1 0 0 0 0 0 0 0 2 ...
## ..$ SRR1792687: int [1:58302] 2 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792688: int [1:58302] 39 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR1792689: int [1:58302] 17 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792690: int [1:58302] 2 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792691: int [1:58302] 25 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792692: int [1:58302] 7 37 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792693: int [1:58302] 0 68 30 0 0 0 0 0 0 3 ...
## ..$ SRR1792694: int [1:58302] 10 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR1792695: int [1:58302] 26 10 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792696: int [1:58302] 6 24 0 0 0 0 0 0 0 5 ...
## ..$ SRR1792697: int [1:58302] 24 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792698: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792699: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792700: int [1:58302] 11 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792701: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792702: int [1:58302] 180 0 0 0 0 0 0 5 0 0 ...
## ..$ SRR1792703: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792704: int [1:58302] 17 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792705: int [1:58302] 7 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792706: int [1:58302] 18 18 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792707: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792708: int [1:58302] 50 8 0 0 0 0 0 0 0 4 ...
## ..$ SRR2981913: int [1:58302] 1 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR2981929: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 34 variables:
## ..$ SRR1792677: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792678: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792679: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792680: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792681: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792682: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792683: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792684: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792685: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792686: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792687: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792688: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792689: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792690: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792691: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792692: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792693: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792694: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792695: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792696: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792697: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792698: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792699: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792700: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792701: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792702: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792703: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792704: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792705: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792706: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792707: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1792708: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR2981913: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR2981929: 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 34 variables:
## ..$ SRR1792677: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792678: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792679: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792680: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792681: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792682: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792683: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792684: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792685: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792686: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792687: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792688: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792689: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792690: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792691: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792692: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792693: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792694: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792695: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792696: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792697: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792698: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792699: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792700: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792701: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792702: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792703: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792704: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792705: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792706: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792707: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR1792708: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR2981913: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR2981929: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## $ MetadataSummary:'data.frame': 34 obs. of 7 variables:
## ..$ QC_summary : chr [1:34] "WARN(6,8)" "WARN(6,8)" "WARN(6,8)" "WARN(6,8)" ...
## ..$ SRX_accession: chr [1:34] "SRX868339" "SRX868340" "SRX868341" "SRX868342" ...
## ..$ SRS_accession: chr [1:34] "SRS839234" "SRS839233" "SRS839232" "SRS839230" ...
## ..$ SRP_accession: chr [1:34] "SRP053296" "SRP053296" "SRP053296" "SRP053296" ...
## ..$ Sample_name : chr [1:34] "GSM1603316" "GSM1603317" "GSM1603318" "GSM1603319" ...
## ..$ GEO_series : chr [1:34] "GSE65705" "GSE65705" "GSE65705" "GSE65705" ...
## ..$ Library_name : logi [1:34] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 34 obs. of 52 variables:
## ..$ QC_summary : chr [1:34] "WARN(6,8)" "WARN(6,8)" "WARN(6,8)" "WARN(6,8)" ...
## ..$ SRX_accession : chr [1:34] "SRX868339" "SRX868340" "SRX868341" "SRX868342" ...
## ..$ SRS_accession : chr [1:34] "SRS839234" "SRS839233" "SRS839232" "SRS839230" ...
## ..$ SRP_accession : chr [1:34] "SRP053296" "SRP053296" "SRP053296" "SRP053296" ...
## ..$ Sample_name : chr [1:34] "GSM1603316" "GSM1603317" "GSM1603318" "GSM1603319" ...
## ..$ GEO_series : chr [1:34] "GSE65705" "GSE65705" "GSE65705" "GSE65705" ...
## ..$ Library_name : logi [1:34] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:34] "GSM1603316" "GSM1603317" "GSM1603318" "GSM1603319" ...
## ..$ ReleaseDate : chr [1:34] "2015-09-15 16:10:16" "2015-09-15 16:10:16" "2015-09-15 16:10:16" "2015-09-15 16:10:16" ...
## ..$ LoadDate : chr [1:34] "2019-03-08 17:19:40" "2015-02-06 12:46:08" "2015-02-06 12:05:31" "2015-02-06 12:02:36" ...
## ..$ spots : int [1:34] 100550061 142776812 59081658 55026871 91839016 78463990 93440864 92788586 79781395 68062166 ...
## ..$ bases : num [1:34] 1.51e+10 2.14e+10 8.86e+09 8.25e+09 1.38e+10 ...
## ..$ spots_with_mates : int [1:34] 100550061 0 59081658 0 0 0 93440864 0 0 0 ...
## ..$ avgLength : int [1:34] 150 150 150 150 150 150 150 150 150 150 ...
## ..$ size_MB : int [1:34] 6757 10078 3864 3388 6583 5428 6667 6231 5417 4150 ...
## ..$ AssemblyName : chr [1:34] "GCA_000001405.13" "GCA_000001405.13" "GCA_000001405.13" "GCA_000001405.13" ...
## ..$ download_path : chr [1:34] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792677/SRR1792677.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792678/SRR1792678.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792679/SRR1792679.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR1792680/SRR1792680.1" ...
## ..$ LibraryName : logi [1:34] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:34] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:34] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:34] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:34] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:34] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:34] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:34] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:34] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:34] "SRP053296" "SRP053296" "SRP053296" "SRP053296" ...
## ..$ BioProject : chr [1:34] "PRJNA274751" "PRJNA274751" "PRJNA274751" "PRJNA274751" ...
## ..$ Study_Pubmed_id : int [1:34] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:34] 274751 274751 274751 274751 274751 274751 274751 274751 274751 274751 ...
## ..$ Sample : chr [1:34] "SRS839234" "SRS839233" "SRS839232" "SRS839230" ...
## ..$ BioSample : chr [1:34] "SAMN03332119" "SAMN03332120" "SAMN03332116" "SAMN03332117" ...
## ..$ SampleType : chr [1:34] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:34] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:34] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:34] NA NA NA NA NA NA ...
## ..$ source : logi [1:34] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:34] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:34] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:34] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:34] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:34] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:34] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:34] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:34] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:34] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:34] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:34] "SRA236686" "SRA236686" "SRA236686" "SRA236686" ...
## ..$ dbgap_study_accession: logi [1:34] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:34] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:34] "BDB1C3EA589E6B570460A1E372F858DF" "815CFF927C2EC57287E6F3CF468AA5C2" "D6BC9E147B4F4ACCFABD99FCFEA1564A" "A279A2B8FC7934E08195076164D81F84" ...
## ..$ ReadHash : chr [1:34] "B2CBB048F149271949652A315428A214" "D69FCB42C282A8252D8531DA2134AC23" "E86708739640DBBB27ED0A005CA6BE3D" "BDF82850B30238D789A1B5CA0EF9588D" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 1952 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP057147: RNA expression of H9 derived cardiomyocytes - scrambled control versus siRNA-mediated knockdown of PANCR: scrambled control; SRX994674, SRX994675, SRX994676: siRNA knockdown PANCR; SRX994677, SRX994679, SRX994680;## 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:
## ..$ SRR1973398: int [1:58302] 0 29 6 1 0 0 0 0 0 2 ...
## ..$ SRR1973399: int [1:58302] 0 20 4 0 0 0 0 0 0 0 ...
## ..$ SRR1973400: int [1:58302] 0 32 3 1 0 0 0 0 0 0 ...
## ..$ SRR1973401: int [1:58302] 0 35 4 1 0 0 0 0 0 4 ...
## ..$ SRR1973402: int [1:58302] 0 37 4 1 0 0 0 0 0 4 ...
## ..$ SRR1973403: int [1:58302] 0 35 1 0 0 0 0 0 0 2 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1973398: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973399: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973400: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973401: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973402: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973403: 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:
## ..$ SRR1973398: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973399: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973400: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973401: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973402: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973403: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX994674" "SRX994675" "SRX994676" "SRX994677" ...
## ..$ SRS_accession: chr [1:6] "SRS909181" "SRS909179" "SRS909178" "SRS909177" ...
## ..$ SRP_accession: chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657075" "GSM1657076" "GSM1657077" "GSM1657078" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ 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] "SRX994674" "SRX994675" "SRX994676" "SRX994677" ...
## ..$ SRS_accession : chr [1:6] "SRS909181" "SRS909179" "SRS909178" "SRS909177" ...
## ..$ SRP_accession : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657075" "GSM1657076" "GSM1657077" "GSM1657078" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1657075" "GSM1657076" "GSM1657077" "GSM1657078" ...
## ..$ ReleaseDate : chr [1:6] "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" ...
## ..$ LoadDate : chr [1:6] "2015-04-14 15:06:16" "2015-04-14 15:08:16" "2015-04-14 15:06:13" "2015-04-14 15:04:42" ...
## ..$ spots : int [1:6] 30619692 24624220 25672396 28014592 27762044 32000000
## ..$ bases : num [1:6] 4.32e+09 3.47e+09 3.62e+09 3.95e+09 3.91e+09 ...
## ..$ spots_with_mates : int [1:6] 30619692 24624220 25672396 28014592 27762044 32000000
## ..$ avgLength : int [1:6] 141 141 141 141 141 141
## ..$ size_MB : int [1:6] 1854 1496 1553 1692 1681 1928
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973398/SRR1973398.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973399/SRR1973399.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973400/SRR1973400.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973401/SRR1973401.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ BioProject : chr [1:6] "PRJNA281062" "PRJNA281062" "PRJNA281062" "PRJNA281062" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 281062 281062 281062 281062 281062 281062
## ..$ Sample : chr [1:6] "SRS909181" "SRS909179" "SRS909178" "SRS909177" ...
## ..$ BioSample : chr [1:6] "SAMN03481903" "SAMN03481904" "SAMN03481905" "SAMN03481906" ...
## ..$ 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] "SRA258577" "SRA258577" "SRA258577" "SRA258577" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "59DFF88F228C64A2CAB835B58DE02624" "4BDD3C0854CB6703D1C29CCE5FA56984" "FFFBEE7C5481C93A72C2A8A5ED0F0FFE" "8A7D0BBF4581A28B3D221ACFD7860EB4" ...
## ..$ ReadHash : chr [1:6] "98ED871F6123160A6083FB0B77CB3E86" "5CA4AD3A1ED6D6F5180B54045C555FF6" "ADE82C8370BB77DF3A15C8B5016D1A6A" "9F499A1C82BD34FB188E5C1DAD611B17" ...
## $ 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
## SRP057147: RNA expression of H9 derived cardiomyocytes - scrambled control versus siRNA-mediated knockdown of PITX2: scrambled control; SRX994674, SRX994675, SRX994676: siRNA knockdown PITX2; SRX994681, SRX994682, SRX994683;## 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:
## ..$ SRR1973398: int [1:58302] 0 29 6 1 0 0 0 0 0 2 ...
## ..$ SRR1973399: int [1:58302] 0 20 4 0 0 0 0 0 0 0 ...
## ..$ SRR1973400: int [1:58302] 0 32 3 1 0 0 0 0 0 0 ...
## ..$ SRR1973404: int [1:58302] 0 29 4 1 0 0 0 0 0 3 ...
## ..$ SRR1973405: int [1:58302] 0 30 6 0 0 0 0 0 0 6 ...
## ..$ SRR1973406: int [1:58302] 0 28 5 1 0 0 0 0 0 2 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1973398: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973399: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973400: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973404: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973405: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973406: 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:
## ..$ SRR1973398: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973399: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973400: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973404: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973405: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973406: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX994674" "SRX994675" "SRX994676" "SRX994681" ...
## ..$ SRS_accession: chr [1:6] "SRS909181" "SRS909179" "SRS909178" "SRS909174" ...
## ..$ SRP_accession: chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657075" "GSM1657076" "GSM1657077" "GSM1657081" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ 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] "SRX994674" "SRX994675" "SRX994676" "SRX994681" ...
## ..$ SRS_accession : chr [1:6] "SRS909181" "SRS909179" "SRS909178" "SRS909174" ...
## ..$ SRP_accession : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657075" "GSM1657076" "GSM1657077" "GSM1657081" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1657075" "GSM1657076" "GSM1657077" "GSM1657081" ...
## ..$ ReleaseDate : chr [1:6] "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" ...
## ..$ LoadDate : chr [1:6] "2015-04-14 15:06:16" "2015-04-14 15:08:16" "2015-04-14 15:06:13" "2015-04-14 15:07:48" ...
## ..$ spots : int [1:6] 30619692 24624220 25672396 28275548 31865541 30052395
## ..$ bases : num [1:6] 4.32e+09 3.47e+09 3.62e+09 3.99e+09 4.49e+09 ...
## ..$ spots_with_mates : int [1:6] 30619692 24624220 25672396 28275548 31865541 30052395
## ..$ avgLength : int [1:6] 141 141 141 141 141 141
## ..$ size_MB : int [1:6] 1854 1496 1553 1708 1926 1826
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973398/SRR1973398.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973399/SRR1973399.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973400/SRR1973400.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973404/SRR1973404.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ BioProject : chr [1:6] "PRJNA281062" "PRJNA281062" "PRJNA281062" "PRJNA281062" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 281062 281062 281062 281062 281062 281062
## ..$ Sample : chr [1:6] "SRS909181" "SRS909179" "SRS909178" "SRS909174" ...
## ..$ BioSample : chr [1:6] "SAMN03481903" "SAMN03481904" "SAMN03481905" "SAMN03481909" ...
## ..$ 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] "SRA258577" "SRA258577" "SRA258577" "SRA258577" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "59DFF88F228C64A2CAB835B58DE02624" "4BDD3C0854CB6703D1C29CCE5FA56984" "FFFBEE7C5481C93A72C2A8A5ED0F0FFE" "656B75DFFB805D31E1BC5BF6A3720B13" ...
## ..$ ReadHash : chr [1:6] "98ED871F6123160A6083FB0B77CB3E86" "5CA4AD3A1ED6D6F5180B54045C555FF6" "ADE82C8370BB77DF3A15C8B5016D1A6A" "DB6516F17DED07B521974C1019D408AA" ...
## $ 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
## SRP057147: RNA expression of H9 derived cardiomyocytes - siRNA-mediated knockdown of PANCR versus siRNA-mediated knockdown of PITX2: siRNA knockdown PANCR; SRX994677, SRX994679, SRX994680: siRNA knockdown PITX2; SRX994681, SRX994682, SRX994683;## 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:
## ..$ SRR1973401: int [1:58302] 0 35 4 1 0 0 0 0 0 4 ...
## ..$ SRR1973402: int [1:58302] 0 37 4 1 0 0 0 0 0 4 ...
## ..$ SRR1973403: int [1:58302] 0 35 1 0 0 0 0 0 0 2 ...
## ..$ SRR1973404: int [1:58302] 0 29 4 1 0 0 0 0 0 3 ...
## ..$ SRR1973405: int [1:58302] 0 30 6 0 0 0 0 0 0 6 ...
## ..$ SRR1973406: int [1:58302] 0 28 5 1 0 0 0 0 0 2 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1973401: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973402: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973403: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973404: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973405: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973406: 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:
## ..$ SRR1973401: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973402: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973403: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973404: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973405: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## ..$ SRR1973406: chr [1:30] "PE" "Sanger/Illumina1.9" "70" "70" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:6] "SRX994677" "SRX994679" "SRX994680" "SRX994681" ...
## ..$ SRS_accession: chr [1:6] "SRS909177" "SRS909176" "SRS909173" "SRS909174" ...
## ..$ SRP_accession: chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657078" "GSM1657079" "GSM1657080" "GSM1657081" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ 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] "SRX994677" "SRX994679" "SRX994680" "SRX994681" ...
## ..$ SRS_accession : chr [1:6] "SRS909177" "SRS909176" "SRS909173" "SRS909174" ...
## ..$ SRP_accession : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657078" "GSM1657079" "GSM1657080" "GSM1657081" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1657078" "GSM1657079" "GSM1657080" "GSM1657081" ...
## ..$ ReleaseDate : chr [1:6] "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" ...
## ..$ LoadDate : chr [1:6] "2015-04-14 15:04:42" "2015-04-14 15:08:03" "2015-04-14 15:10:28" "2015-04-14 15:07:48" ...
## ..$ spots : int [1:6] 28014592 27762044 32000000 28275548 31865541 30052395
## ..$ bases : num [1:6] 3.95e+09 3.91e+09 4.51e+09 3.99e+09 4.49e+09 ...
## ..$ spots_with_mates : int [1:6] 28014592 27762044 32000000 28275548 31865541 30052395
## ..$ avgLength : int [1:6] 141 141 141 141 141 141
## ..$ size_MB : int [1:6] 1692 1681 1928 1708 1926 1826
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973401/SRR1973401.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973402/SRR1973402.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973403/SRR1973403.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973404/SRR1973404.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ BioProject : chr [1:6] "PRJNA281062" "PRJNA281062" "PRJNA281062" "PRJNA281062" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 281062 281062 281062 281062 281062 281062
## ..$ Sample : chr [1:6] "SRS909177" "SRS909176" "SRS909173" "SRS909174" ...
## ..$ BioSample : chr [1:6] "SAMN03481906" "SAMN03481907" "SAMN03481908" "SAMN03481909" ...
## ..$ 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] "SRA258577" "SRA258577" "SRA258577" "SRA258577" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "8A7D0BBF4581A28B3D221ACFD7860EB4" "DA7A163254F5E1B47B1D0223DB4EFB1A" "C365ED1785BD64617E7422BA5CB0803B" "656B75DFFB805D31E1BC5BF6A3720B13" ...
## ..$ ReadHash : chr [1:6] "9F499A1C82BD34FB188E5C1DAD611B17" "EF0E731DA2E3C53A7C9B57C40B4B5017" "60C727EC0DA517CE3EF3D8A4789164F0" "DB6516F17DED07B521974C1019D408AA" ...
## $ 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
## SRP057147: smallRNA expression of H9 derived cardiomyocytes - scrambled control versus siRNA-mediated knockdown of PANCR: scrambled control; SRX994684, SRX994685, SRX994686: siRNA knockdown PANCR; SRX994687, SRX994688, SRX994689;## 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:
## ..$ SRR1973407: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973408: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973409: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973410: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973411: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973412: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1973407: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973408: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973409: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973410: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973411: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973412: 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:
## ..$ SRR1973407: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973408: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973409: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973410: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973411: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973412: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(4,5,6,7)" "FAIL(1,4,5,6,7)" "FAIL(4,5,6,7)" "FAIL(4,5,6,7)" ...
## ..$ SRX_accession: chr [1:6] "SRX994684" "SRX994685" "SRX994686" "SRX994687" ...
## ..$ SRS_accession: chr [1:6] "SRS909170" "SRS909169" "SRS909168" "SRS909162" ...
## ..$ SRP_accession: chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657084" "GSM1657085" "GSM1657086" "GSM1657087" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ 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(4,5,6,7)" "FAIL(1,4,5,6,7)" "FAIL(4,5,6,7)" "FAIL(4,5,6,7)" ...
## ..$ SRX_accession : chr [1:6] "SRX994684" "SRX994685" "SRX994686" "SRX994687" ...
## ..$ SRS_accession : chr [1:6] "SRS909170" "SRS909169" "SRS909168" "SRS909162" ...
## ..$ SRP_accession : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657084" "GSM1657085" "GSM1657086" "GSM1657087" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1657084" "GSM1657085" "GSM1657086" "GSM1657087" ...
## ..$ ReleaseDate : chr [1:6] "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" ...
## ..$ LoadDate : chr [1:6] "2015-04-14 14:58:15" "2015-04-14 14:58:12" "2015-04-14 14:58:17" "2015-04-14 14:59:36" ...
## ..$ spots : int [1:6] 1337049 1221820 1589718 1694309 445531 1304687
## ..$ bases : int [1:6] 32166857 29264104 38547243 40470185 10750239 30877281
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 24 23 24 23 24 23
## ..$ size_MB : int [1:6] 17 15 20 21 5 16
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973407/SRR1973407.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973408/SRR1973408.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973409/SRR1973409.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973410/SRR1973410.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina MiSeq" "Illumina MiSeq" "Illumina MiSeq" "Illumina MiSeq" ...
## ..$ SRAStudy : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ BioProject : chr [1:6] "PRJNA281062" "PRJNA281062" "PRJNA281062" "PRJNA281062" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 281062 281062 281062 281062 281062 281062
## ..$ Sample : chr [1:6] "SRS909170" "SRS909169" "SRS909168" "SRS909162" ...
## ..$ BioSample : chr [1:6] "SAMN03481912" "SAMN03481913" "SAMN03481914" "SAMN03481915" ...
## ..$ 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] "SRA258577" "SRA258577" "SRA258577" "SRA258577" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "C28CD814B3CE42BFF88CD31F2E214799" "3B4EB497E115891C09C9BE8B98FE6756" "2ED7A06CF94F5BD0090F7F48CCCF389C" "1285DA8670B669F435837960CF27BF79" ...
## ..$ ReadHash : chr [1:6] "C9539742B072648D91981466EA69E0D9" "5345F22B9C7A33E44340E0C081D22AB3" "8B466419B911DA6A34E573F86E9FDCA3" "9D7972F9FA829594C73CB358D858749B" ...
## $ absent : chr(0)## SRP057147: smallRNA expression of H9 derived cardiomyocytes - scrambled control versus siRNA-mediated knockdown of PITX2: scrambled control; SRX994684, SRX994685, SRX994686: siRNA knockdown PITX2; SRX994690, SRX994691, SRX994692;
## 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:
## ..$ SRR1973407: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973408: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973409: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973413: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973414: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973415: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1973407: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973408: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973409: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973413: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973414: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973415: 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:
## ..$ SRR1973407: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973408: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973409: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973413: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973414: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973415: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(4,5,6,7)" "FAIL(1,4,5,6,7)" "FAIL(4,5,6,7)" "FAIL(4,5,6,7)" ...
## ..$ SRX_accession: chr [1:6] "SRX994684" "SRX994685" "SRX994686" "SRX994690" ...
## ..$ SRS_accession: chr [1:6] "SRS909170" "SRS909169" "SRS909168" "SRS909163" ...
## ..$ SRP_accession: chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657084" "GSM1657085" "GSM1657086" "GSM1657090" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ 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(4,5,6,7)" "FAIL(1,4,5,6,7)" "FAIL(4,5,6,7)" "FAIL(4,5,6,7)" ...
## ..$ SRX_accession : chr [1:6] "SRX994684" "SRX994685" "SRX994686" "SRX994690" ...
## ..$ SRS_accession : chr [1:6] "SRS909170" "SRS909169" "SRS909168" "SRS909163" ...
## ..$ SRP_accession : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657084" "GSM1657085" "GSM1657086" "GSM1657090" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1657084" "GSM1657085" "GSM1657086" "GSM1657090" ...
## ..$ ReleaseDate : chr [1:6] "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" ...
## ..$ LoadDate : chr [1:6] "2015-04-14 14:58:15" "2015-04-14 14:58:12" "2015-04-14 14:58:17" "2015-04-14 14:58:13" ...
## ..$ spots : int [1:6] 1337049 1221820 1589718 1523502 1196175 1003898
## ..$ bases : int [1:6] 32166857 29264104 38547243 36224825 28634117 24182776
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 24 23 24 23 23 24
## ..$ size_MB : int [1:6] 17 15 20 19 15 13
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973407/SRR1973407.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973408/SRR1973408.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973409/SRR1973409.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973413/SRR1973413.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina MiSeq" "Illumina MiSeq" "Illumina MiSeq" "Illumina MiSeq" ...
## ..$ SRAStudy : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ BioProject : chr [1:6] "PRJNA281062" "PRJNA281062" "PRJNA281062" "PRJNA281062" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 281062 281062 281062 281062 281062 281062
## ..$ Sample : chr [1:6] "SRS909170" "SRS909169" "SRS909168" "SRS909163" ...
## ..$ BioSample : chr [1:6] "SAMN03481912" "SAMN03481913" "SAMN03481914" "SAMN03481918" ...
## ..$ 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] "SRA258577" "SRA258577" "SRA258577" "SRA258577" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "C28CD814B3CE42BFF88CD31F2E214799" "3B4EB497E115891C09C9BE8B98FE6756" "2ED7A06CF94F5BD0090F7F48CCCF389C" "92F1E88685362DA2461B38DA19AA8CDE" ...
## ..$ ReadHash : chr [1:6] "C9539742B072648D91981466EA69E0D9" "5345F22B9C7A33E44340E0C081D22AB3" "8B466419B911DA6A34E573F86E9FDCA3" "54AA563EF1F115AAB6D2835C0AB7BBD0" ...
## $ absent : chr(0)## SRP057147: smallRNA expression of H9 derived cardiomyocytes - siRNA-mediated knockdown of PANCR versus siRNA-mediated knockdown of PITX2: siRNA knockdown PANCR; SRX994687, SRX994688, SRX994689: siRNA knockdown PITX2; SRX994690, SRX994691, SRX994692;
## 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:
## ..$ SRR1973410: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973411: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973412: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973413: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973414: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973415: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR1973410: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973411: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973412: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973413: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973414: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR1973415: 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:
## ..$ SRR1973410: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973411: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973412: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973413: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973414: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## ..$ SRR1973415: chr [1:30] "SE" "Sanger/Illumina1.9" "20" "22" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "FAIL(4,5,6,7)" "FAIL(1,4,5,6,7)" "FAIL(1,4,5,6,7)" "FAIL(4,5,6,7)" ...
## ..$ SRX_accession: chr [1:6] "SRX994687" "SRX994688" "SRX994689" "SRX994690" ...
## ..$ SRS_accession: chr [1:6] "SRS909162" "SRS909166" "SRS909167" "SRS909163" ...
## ..$ SRP_accession: chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657087" "GSM1657088" "GSM1657089" "GSM1657090" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ 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(4,5,6,7)" "FAIL(1,4,5,6,7)" "FAIL(1,4,5,6,7)" "FAIL(4,5,6,7)" ...
## ..$ SRX_accession : chr [1:6] "SRX994687" "SRX994688" "SRX994689" "SRX994690" ...
## ..$ SRS_accession : chr [1:6] "SRS909162" "SRS909166" "SRS909167" "SRS909163" ...
## ..$ SRP_accession : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ Sample_name : chr [1:6] "GSM1657087" "GSM1657088" "GSM1657089" "GSM1657090" ...
## ..$ GEO_series : chr [1:6] "GSE67844" "GSE67844" "GSE67844" "GSE67844" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM1657087" "GSM1657088" "GSM1657089" "GSM1657090" ...
## ..$ ReleaseDate : chr [1:6] "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" "2015-06-16 10:53:10" ...
## ..$ LoadDate : chr [1:6] "2015-04-14 14:59:36" "2015-04-14 14:58:03" "2015-04-14 14:58:11" "2015-04-14 14:58:13" ...
## ..$ spots : int [1:6] 1694309 445531 1304687 1523502 1196175 1003898
## ..$ bases : int [1:6] 40470185 10750239 30877281 36224825 28634117 24182776
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 23 24 23 23 23 24
## ..$ size_MB : int [1:6] 21 5 16 19 15 13
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973410/SRR1973410.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973411/SRR1973411.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973412/SRR1973412.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1973413/SRR1973413.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina MiSeq" "Illumina MiSeq" "Illumina MiSeq" "Illumina MiSeq" ...
## ..$ SRAStudy : chr [1:6] "SRP057147" "SRP057147" "SRP057147" "SRP057147" ...
## ..$ BioProject : chr [1:6] "PRJNA281062" "PRJNA281062" "PRJNA281062" "PRJNA281062" ...
## ..$ Study_Pubmed_id : int [1:6] 2 2 2 2 2 2
## ..$ ProjectID : int [1:6] 281062 281062 281062 281062 281062 281062
## ..$ Sample : chr [1:6] "SRS909162" "SRS909166" "SRS909167" "SRS909163" ...
## ..$ BioSample : chr [1:6] "SAMN03481915" "SAMN03481916" "SAMN03481917" "SAMN03481918" ...
## ..$ 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] "SRA258577" "SRA258577" "SRA258577" "SRA258577" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "1285DA8670B669F435837960CF27BF79" "DA08EE0F921946E53C0C8FDD3F803C03" "0C9C50DE25BECF4D66B6C6F4433FF6C0" "92F1E88685362DA2461B38DA19AA8CDE" ...
## ..$ ReadHash : chr [1:6] "9D7972F9FA829594C73CB358D858749B" "C26CA8E991EB0AE5B35DF9A987FB92D9" "B52385D28764E7C65DB02B54E31147A4" "54AA563EF1F115AAB6D2835C0AB7BBD0" ...
## $ absent : chr(0)## SRP068292: normal aortic tricuspid valve control versus calcified aortic tricuspid valve: control; SRX1526945, SRX1526946, SRX1526947, SRX1526948, SRX1526949, SRX1526950, SRX1526951, SRX1526952, SRX1526953: calcified aortic tricuspid valve; SRX1526936, SRX1526937, SRX1526938, SRX1526939, SRX1526940, SRX1526941, SRX1526942, SRX1526943, SRX1526944
## 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 17 variables:
## ..$ SRR3096626: int [1:58302] 1 12 1 0 0 0 0 0 0 0 ...
## ..$ SRR3096627: int [1:58302] 0 20 0 1 0 0 0 0 0 1 ...
## ..$ SRR3096628: int [1:58302] 0 32 2 0 0 0 0 0 0 0 ...
## ..$ SRR3096629: int [1:58302] 0 32 0 0 0 0 0 0 0 1 ...
## ..$ SRR3096630: int [1:58302] 0 20 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096631: int [1:58302] 1 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096632: int [1:58302] 0 76 2 0 0 0 0 0 0 0 ...
## ..$ SRR3096633: int [1:58302] 0 14 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096634: int [1:58302] 0 39 1 2 0 0 0 0 0 0 ...
## ..$ SRR3096635: int [1:58302] 0 16 1 0 0 0 0 0 0 0 ...
## ..$ SRR3096636: int [1:58302] 0 20 0 0 0 0 0 0 0 1 ...
## ..$ SRR3096637: int [1:58302] 1 43 0 4 0 1 0 0 0 0 ...
## ..$ SRR3096638: int [1:58302] 0 19 0 1 0 0 0 0 0 2 ...
## ..$ SRR3096639: int [1:58302] 0 10 1 0 0 0 0 0 0 0 ...
## ..$ SRR3096640: int [1:58302] 0 19 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096641: int [1:58302] 0 54 2 0 0 0 0 0 0 2 ...
## ..$ SRR3096642: int [1:58302] 0 67 3 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 17 variables:
## ..$ SRR3096626: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096627: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096628: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096629: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096630: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096631: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096632: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096633: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096634: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096635: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096636: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096637: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096638: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096639: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096640: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096641: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR3096642: 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 17 variables:
## ..$ SRR3096626: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096627: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096628: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096629: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096630: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096631: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096632: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096633: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096634: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096635: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096636: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096637: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096638: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096639: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096640: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096641: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR3096642: chr [1:30] "PE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 17 obs. of 7 variables:
## ..$ QC_summary : chr [1:17] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:17] "SRX1526936" "SRX1526937" "SRX1526938" "SRX1526939" ...
## ..$ SRS_accession: chr [1:17] "SRS1244792" "SRS1244791" "SRS1244790" "SRS1244789" ...
## ..$ SRP_accession: chr [1:17] "SRP068292" "SRP068292" "SRP068292" "SRP068292" ...
## ..$ Sample_name : chr [1:17] "GSM2036523" "GSM2036524" "GSM2036525" "GSM2036526" ...
## ..$ GEO_series : chr [1:17] "GSE76717" "GSE76717" "GSE76717" "GSE76717" ...
## ..$ Library_name : logi [1:17] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 17 obs. of 52 variables:
## ..$ QC_summary : chr [1:17] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:17] "SRX1526936" "SRX1526937" "SRX1526938" "SRX1526939" ...
## ..$ SRS_accession : chr [1:17] "SRS1244792" "SRS1244791" "SRS1244790" "SRS1244789" ...
## ..$ SRP_accession : chr [1:17] "SRP068292" "SRP068292" "SRP068292" "SRP068292" ...
## ..$ Sample_name : chr [1:17] "GSM2036523" "GSM2036524" "GSM2036525" "GSM2036526" ...
## ..$ GEO_series : chr [1:17] "GSE76717" "GSE76717" "GSE76717" "GSE76717" ...
## ..$ Library_name : logi [1:17] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:17] "GSM2036523" "GSM2036524" "GSM2036525" "GSM2036526" ...
## ..$ ReleaseDate : chr [1:17] "2016-09-22 16:09:08" "2016-09-22 16:09:08" "2016-09-22 16:09:08" "2016-09-22 16:09:08" ...
## ..$ LoadDate : chr [1:17] "2016-11-15 20:21:04" "2016-11-15 20:26:03" "2016-11-15 20:27:56" "2016-11-15 20:18:26" ...
## ..$ spots : int [1:17] 16845663 19240224 26961878 21514202 9053393 9337387 25679508 7723693 39990128 19041490 ...
## ..$ bases : num [1:17] 1.51e+09 1.71e+09 2.40e+09 1.94e+09 8.14e+08 ...
## ..$ spots_with_mates : int [1:17] 13269572 14980613 21006961 17274160 7234261 7180921 19305089 5133852 29928520 14711658 ...
## ..$ avgLength : int [1:17] 89 88 88 90 89 88 87 83 87 88 ...
## ..$ size_MB : int [1:17] 660 750 1205 854 354 361 1143 290 1612 743 ...
## ..$ AssemblyName : chr [1:17] "GCA_000001405.13" "GCA_000001405.13" "GCA_000001405.13" "GCA_000001405.13" ...
## ..$ download_path : chr [1:17] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR3096626/SRR3096626.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR3096627/SRR3096627.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR3096628/SRR3096628.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR3096629/SRR3096629.2" ...
## ..$ LibraryName : logi [1:17] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:17] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:17] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:17] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:17] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:17] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:17] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:17] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:17] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:17] "SRP068292" "SRP068292" "SRP068292" "SRP068292" ...
## ..$ BioProject : chr [1:17] "PRJNA308452" "PRJNA308452" "PRJNA308452" "PRJNA308452" ...
## ..$ Study_Pubmed_id : int [1:17] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:17] 308452 308452 308452 308452 308452 308452 308452 308452 308452 308452 ...
## ..$ Sample : chr [1:17] "SRS1244792" "SRS1244791" "SRS1244790" "SRS1244789" ...
## ..$ BioSample : chr [1:17] "SAMN04395646" "SAMN04395647" "SAMN04395648" "SAMN04395649" ...
## ..$ SampleType : chr [1:17] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:17] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:17] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:17] NA NA NA NA NA NA ...
## ..$ source : logi [1:17] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:17] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:17] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:17] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:17] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:17] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:17] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:17] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:17] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:17] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:17] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:17] "SRA332840" "SRA332840" "SRA332840" "SRA332840" ...
## ..$ dbgap_study_accession: logi [1:17] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:17] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:17] "C00EC5AC5D51DD4AE5A843B1BF783DF4" "436762F83273805485E3C7B3466545D6" "D1DD6152E4ECBD8BEFA4A1994090CD23" "BDB6CC05FAEC722B1188354E2E4171D6" ...
## ..$ ReadHash : chr [1:17] "579ECF024F63E3D66E9FE6DD9E911C31" "225D328C54F13511BED3C6F968BB0439" "12DF036FBFBCDC295E4879B6AEF2E3B5" "4DD5FA8CCCA748B8594EB317FF017B60" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 171 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP081577: control vs TCF21 overexpression in human coronary artery smooth muscle cells: control; SRX2018562, SRX2018563, SRX2018564, SRX2018565: TCF21 overexpression; SRX2018566, SRX2018567, SRX2018568, SRX2018569;## 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:
## ..$ SRR4026603: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR4026604: int [1:58302] 1 2 2 0 0 0 0 0 0 0 ...
## ..$ SRR4026605: int [1:58302] 0 3 1 0 0 0 0 0 0 0 ...
## ..$ SRR4026606: int [1:58302] 0 1 2 1 0 0 0 0 0 1 ...
## ..$ SRR4026607: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026608: int [1:58302] 0 1 0 0 0 0 0 2 0 0 ...
## ..$ SRR4026609: int [1:58302] 0 1 2 0 0 0 0 0 0 0 ...
## ..$ SRR4026610: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026611: int [1:58302] 0 4 3 0 0 0 0 0 0 0 ...
## ..$ SRR4026612: int [1:58302] 0 2 2 0 0 0 0 0 0 0 ...
## ..$ SRR4026613: int [1:58302] 0 4 2 0 0 0 0 0 0 0 ...
## ..$ SRR4026614: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026615: int [1:58302] 0 5 1 0 0 0 0 0 0 2 ...
## ..$ SRR4026616: int [1:58302] 0 4 1 0 0 0 0 0 0 1 ...
## ..$ SRR4026617: int [1:58302] 0 5 2 0 0 0 0 0 0 0 ...
## ..$ SRR4026618: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 16 variables:
## ..$ SRR4026603: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026604: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026605: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026606: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026607: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026608: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026609: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026610: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026611: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026612: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026613: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026614: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026615: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026616: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026617: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR4026618: 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:
## ..$ SRR4026603: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026604: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026605: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026606: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026607: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026608: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026609: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026610: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026611: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026612: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026613: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026614: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026615: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026616: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026617: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR4026618: chr [1:30] "SE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 16 obs. of 7 variables:
## ..$ QC_summary : chr [1:16] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:16] "SRX2018562" "SRX2018562" "SRX2018563" "SRX2018563" ...
## ..$ SRS_accession: chr [1:16] "SRS1614461" "SRS1614461" "SRS1614462" "SRS1614462" ...
## ..$ SRP_accession: chr [1:16] "SRP081577" "SRP081577" "SRP081577" "SRP081577" ...
## ..$ Sample_name : chr [1:16] "GSM2277221" "GSM2277221" "GSM2277223" "GSM2277223" ...
## ..$ GEO_series : chr [1:16] "GSE85565" "GSE85565" "GSE85565" "GSE85565" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 16 obs. of 52 variables:
## ..$ QC_summary : chr [1:16] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:16] "SRX2018562" "SRX2018562" "SRX2018563" "SRX2018563" ...
## ..$ SRS_accession : chr [1:16] "SRS1614461" "SRS1614461" "SRS1614462" "SRS1614462" ...
## ..$ SRP_accession : chr [1:16] "SRP081577" "SRP081577" "SRP081577" "SRP081577" ...
## ..$ Sample_name : chr [1:16] "GSM2277221" "GSM2277221" "GSM2277223" "GSM2277223" ...
## ..$ GEO_series : chr [1:16] "GSE85565" "GSE85565" "GSE85565" "GSE85565" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:16] "GSM2277221" "GSM2277221" "GSM2277223" "GSM2277223" ...
## ..$ ReleaseDate : chr [1:16] "2017-04-14 13:08:06" "2017-04-14 13:08:06" "2017-04-14 13:08:06" "2017-04-14 13:08:06" ...
## ..$ LoadDate : chr [1:16] "2016-08-12 17:16:49" "2016-08-12 17:16:25" "2016-08-12 17:17:13" "2016-08-12 17:16:11" ...
## ..$ spots : int [1:16] 20132872 20168128 20718846 20761527 21806039 21200734 20228912 19652415 18261577 18318251 ...
## ..$ bases : num [1:16] 2.01e+09 2.02e+09 2.07e+09 2.08e+09 2.18e+09 ...
## ..$ spots_with_mates : int [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:16] 100 100 100 100 100 100 100 100 100 100 ...
## ..$ size_MB : int [1:16] 1195 1191 1224 1219 1285 1227 1184 1130 1078 1076 ...
## ..$ AssemblyName : logi [1:16] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:16] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026603/SRR4026603.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026604/SRR4026604.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026605/SRR4026605.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR4026606/SRR4026606.1" ...
## ..$ LibraryName : logi [1:16] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:16] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:16] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:16] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:16] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:16] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:16] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:16] "SRP081577" "SRP081577" "SRP081577" "SRP081577" ...
## ..$ BioProject : chr [1:16] "PRJNA338802" "PRJNA338802" "PRJNA338802" "PRJNA338802" ...
## ..$ Study_Pubmed_id : int [1:16] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:16] 338802 338802 338802 338802 338802 338802 338802 338802 338802 338802 ...
## ..$ Sample : chr [1:16] "SRS1614461" "SRS1614461" "SRS1614462" "SRS1614462" ...
## ..$ BioSample : chr [1:16] "SAMN05571224" "SAMN05571224" "SAMN05571217" "SAMN05571217" ...
## ..$ 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] "SRA452014" "SRA452014" "SRA452014" "SRA452014" ...
## ..$ dbgap_study_accession: logi [1:16] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:16] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:16] "B4997D0E1B6C7DEAEAC171FFC7A6EF19" "A3DCDB6B88F868780ED69D7769EE3992" "0FCB3BDA1C3BA57C50475B53924BA68B" "B2D47662C37DF568E376C0D15A2A85C5" ...
## ..$ ReadHash : chr [1:16] "FB2174F0A7348B783F4CB64516922828" "BB63A845F93255DAB020ED6B7FAC31FB" "73A519EC5281B6098D80657080581E43" "7F59ECE5F403C9E634E5A7598D67E518" ...
## $ 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
## SRP011923: smallRNA profiles of healthy right verntricle control versus Tetralogy of Fallot (TOF) right ventricle: control; SRX131376, SRX131378, SRX131380, SRX131382: TOF; SRX131383, SRX131385, SRX131386, SRX131387, SRX131388, SRX131389, SRX131390, SRX131391, SRX131392, SRX131393, SRX131394, SRX131395, SRX131396, SRX131397, SRX131398, SRX131399, SRX131400, SRX131401, SRX131402, SRX131403, SRX131404, SRX131405, SRX131406;## 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:
## ..$ SRR448046: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448050: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448052: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448061: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR448046: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448050: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448052: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448061: 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:
## ..$ SRR448046: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448050: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448052: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448061: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## $ 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)"
## ..$ SRX_accession: chr [1:4] "SRX131376" "SRX131380" "SRX131382" "SRX131391"
## ..$ SRS_accession: chr [1:4] "SRS302497" "SRS302501" "SRS302503" "SRS302512"
## ..$ SRP_accession: chr [1:4] "SRP011923" "SRP011923" "SRP011923" "SRP011923"
## ..$ Sample_name : chr [1:4] "GSM900443" "GSM900447" "GSM900449" "GSM900458"
## ..$ GEO_series : chr [1:4] "GSE36759" "GSE36759" "GSE36759" "GSE36759"
## ..$ Library_name : chr [1:4] "GSM900443: NH-02_RV_smallRNA" "GSM900447: NH-06_RV_smallRNA" "GSM900449: NH-08_RV_smallRNA" "GSM900458: TOF-09_RV_smallRNA"
## $ 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)"
## ..$ SRX_accession : chr [1:4] "SRX131376" "SRX131380" "SRX131382" "SRX131391"
## ..$ SRS_accession : chr [1:4] "SRS302497" "SRS302501" "SRS302503" "SRS302512"
## ..$ SRP_accession : chr [1:4] "SRP011923" "SRP011923" "SRP011923" "SRP011923"
## ..$ Sample_name : chr [1:4] "GSM900443" "GSM900447" "GSM900449" "GSM900458"
## ..$ GEO_series : chr [1:4] "GSE36759" "GSE36759" "GSE36759" "GSE36759"
## ..$ Library_name : chr [1:4] "GSM900443: NH-02_RV_smallRNA" "GSM900447: NH-06_RV_smallRNA" "GSM900449: NH-08_RV_smallRNA" "GSM900458: TOF-09_RV_smallRNA"
## ..$ SampleName : chr [1:4] "GSM900443" "GSM900447" "GSM900449" "GSM900458"
## ..$ ReleaseDate : chr [1:4] "2019-12-05 22:24:24" "2019-12-05 22:24:24" "2019-12-05 22:24:24" "2019-12-05 22:24:24"
## ..$ LoadDate : chr [1:4] "2015-06-28 14:27:27" "2015-06-28 14:26:58" "2015-06-28 14:27:06" "2015-06-28 14:26:09"
## ..$ spots : int [1:4] 16270049 14475968 14890970 16226821
## ..$ bases : int [1:4] 585721764 521134848 536074920 584165556
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 36 36 36 36
## ..$ size_MB : int [1:4] 1235 997 1036 933
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR448046/SRR448046.3" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR448050/SRR448050.3" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR448052/SRR448052.3" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR448061/SRR448061.3"
## ..$ LibraryName : chr [1:4] "GSM900443: NH-02_RV_smallRNA" "GSM900447: NH-06_RV_smallRNA" "GSM900449: NH-08_RV_smallRNA" "GSM900458: TOF-09_RV_smallRNA"
## ..$ LibraryStrategy : chr [1:4] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-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] "Illumina Genome Analyzer" "Illumina Genome Analyzer" "Illumina Genome Analyzer" "Illumina Genome Analyzer"
## ..$ SRAStudy : chr [1:4] "SRP011923" "SRP011923" "SRP011923" "SRP011923"
## ..$ BioProject : chr [1:4] "PRJNA156779" "PRJNA156779" "PRJNA156779" "PRJNA156779"
## ..$ Study_Pubmed_id : int [1:4] 3 3 3 3
## ..$ ProjectID : int [1:4] 156779 156779 156779 156779
## ..$ Sample : chr [1:4] "SRS302497" "SRS302501" "SRS302503" "SRS302512"
## ..$ BioSample : chr [1:4] "SAMN00839435" "SAMN00839439" "SAMN00839441" "SAMN00839450"
## ..$ 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] "SRA051265" "SRA051265" "SRA051265" "SRA051265"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "CAB3B1523DE23A9ED656EF465CDC3CA0" "2F6AFED09BDA07B04F3DF7794FEB0A2B" "3FD0A2AC1182BB866BBE0EA311A262A4" "657C91C987F6C69C47652315D608CAD5"
## ..$ ReadHash : chr [1:4] "9F911A2FB22D9521B1ADAD7AB99B0474" "6070F539A3F24E4CB683469EF1935121" "A99490D231CDAB659D40262DF3A909FA" "A398257748C3995322E57D2B202A6789"
## $ absent : chr(0)## SRP011924: mRNA profiles of healthy right verntricle control versus Tetralogy of Fallot (TOF) right ventricle: control; SRX131416, SRX131418, SRX131420: TOF; SRX131421, SRX131422, SRX131423, SRX131424, SRX131425, SRX131426, SRX131427, SRX131428, SRX131429, SRX131430, SRX131431, SRX131432, SRX131433, SRX131434, SRX131435, SRX131436, SRX131437, SRX131438, SRX131439, SRX131440, SRX131441, SRX131442;
## 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 25 variables:
## ..$ SRR448090: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448092: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR448094: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448095: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448096: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448097: int [1:58302] 0 0 0 0 0 0 0 0 0 1 ...
## ..$ SRR448098: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448099: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR448100: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448101: int [1:58302] 0 0 0 1 0 0 0 0 0 0 ...
## ..$ SRR448102: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448103: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448104: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR448105: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448106: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR448107: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448108: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448109: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448110: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448111: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448112: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448113: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR448114: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448115: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR448116: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 25 variables:
## ..$ SRR448090: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448092: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448094: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448095: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448096: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448097: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448098: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448099: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448100: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448101: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448102: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448103: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448104: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448105: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448106: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448107: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448108: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448109: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448110: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448111: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448112: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448113: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448114: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448115: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR448116: 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 25 variables:
## ..$ SRR448090: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448092: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448094: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448095: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448096: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448097: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448098: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448099: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448100: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448101: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448102: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448103: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448104: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448105: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448106: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448107: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448108: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448109: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448110: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448111: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448112: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448113: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448114: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448115: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR448116: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## $ MetadataSummary:'data.frame': 25 obs. of 7 variables:
## ..$ QC_summary : chr [1:25] "WARN(3,4,5,7)" "PASS" "WARN(4)" "WARN(4,5,7)" ...
## ..$ SRX_accession: chr [1:25] "SRX131416" "SRX131418" "SRX131420" "SRX131421" ...
## ..$ SRS_accession: chr [1:25] "SRS302529" "SRS302531" "SRS302533" "SRS302534" ...
## ..$ SRP_accession: chr [1:25] "SRP011924" "SRP011924" "SRP011924" "SRP011924" ...
## ..$ Sample_name : chr [1:25] "GSM900478" "GSM900480" "GSM900482" "GSM900483" ...
## ..$ GEO_series : chr [1:25] "GSE36761" "GSE36761" "GSE36761" "GSE36761" ...
## ..$ Library_name : chr [1:25] "GSM900478: NH-04_RV_mRNA" "GSM900480: NH-06_RV_mRNA" "GSM900482: NH-08_RV_mRNA" "GSM900483: TOF-01_RV_mRNA" ...
## $ MetadataFull :'data.frame': 25 obs. of 52 variables:
## ..$ QC_summary : chr [1:25] "WARN(3,4,5,7)" "PASS" "WARN(4)" "WARN(4,5,7)" ...
## ..$ SRX_accession : chr [1:25] "SRX131416" "SRX131418" "SRX131420" "SRX131421" ...
## ..$ SRS_accession : chr [1:25] "SRS302529" "SRS302531" "SRS302533" "SRS302534" ...
## ..$ SRP_accession : chr [1:25] "SRP011924" "SRP011924" "SRP011924" "SRP011924" ...
## ..$ Sample_name : chr [1:25] "GSM900478" "GSM900480" "GSM900482" "GSM900483" ...
## ..$ GEO_series : chr [1:25] "GSE36761" "GSE36761" "GSE36761" "GSE36761" ...
## ..$ Library_name : chr [1:25] "GSM900478: NH-04_RV_mRNA" "GSM900480: NH-06_RV_mRNA" "GSM900482: NH-08_RV_mRNA" "GSM900483: TOF-01_RV_mRNA" ...
## ..$ SampleName : chr [1:25] "GSM900478" "GSM900480" "GSM900482" "GSM900483" ...
## ..$ ReleaseDate : chr [1:25] "2014-02-04 16:47:08" "2014-02-04 16:47:08" "2014-02-04 16:47:08" "2014-02-04 16:47:08" ...
## ..$ LoadDate : chr [1:25] "2015-06-28 14:23:30" "2015-06-28 14:24:19" "2015-06-28 14:25:13" "2015-06-28 14:23:07" ...
## ..$ spots : int [1:25] 12961101 20296818 23597799 10888508 19907118 21882581 23167354 14570039 21750958 18392413 ...
## ..$ bases : int [1:25] 466599636 730685448 849520764 391986288 716656248 787772916 834024744 524521404 783034488 662126868 ...
## ..$ spots_with_mates : int [1:25] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:25] 36 36 36 36 36 36 36 36 36 36 ...
## ..$ size_MB : int [1:25] 259 519 1172 154 570 907 988 217 906 599 ...
## ..$ AssemblyName : logi [1:25] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:25] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR448090/SRR448090.3" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR448092/SRR448092.3" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR448094/SRR448094.3" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR448095/SRR448095.3" ...
## ..$ LibraryName : chr [1:25] "GSM900478: NH-04_RV_mRNA" "GSM900480: NH-06_RV_mRNA" "GSM900482: NH-08_RV_mRNA" "GSM900483: TOF-01_RV_mRNA" ...
## ..$ LibraryStrategy : chr [1:25] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:25] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:25] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:25] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:25] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:25] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:25] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:25] "Illumina Genome Analyzer" "Illumina Genome Analyzer" "Illumina Genome Analyzer" "Illumina Genome Analyzer" ...
## ..$ SRAStudy : chr [1:25] "SRP011924" "SRP011924" "SRP011924" "SRP011924" ...
## ..$ BioProject : chr [1:25] "PRJNA156781" "PRJNA156781" "PRJNA156781" "PRJNA156781" ...
## ..$ Study_Pubmed_id : int [1:25] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:25] 156781 156781 156781 156781 156781 156781 156781 156781 156781 156781 ...
## ..$ Sample : chr [1:25] "SRS302529" "SRS302531" "SRS302533" "SRS302534" ...
## ..$ BioSample : chr [1:25] "SAMN00839467" "SAMN00839469" "SAMN00839471" "SAMN00839472" ...
## ..$ SampleType : chr [1:25] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:25] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:25] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:25] NA NA NA NA NA NA ...
## ..$ source : logi [1:25] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:25] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:25] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:25] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:25] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:25] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:25] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:25] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:25] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:25] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:25] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:25] "SRA051266" "SRA051266" "SRA051266" "SRA051266" ...
## ..$ dbgap_study_accession: logi [1:25] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:25] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:25] "3E8CD3B7E12024423B1217F838B3A71E" "0BE96D696619D0DEB17F12778B21B8A1" "A47F6AAC6C97B0C74EE1316C46C24228" "526F18F27D638CD097FEE1BAF2138FE5" ...
## ..$ ReadHash : chr [1:25] "54383526C5E06DC73D62413CAA0CB932" "81999246D5D2208D4FAF854F362B8A49" "D378F2AA36819AF437F380252292E340" "68A2008DFAFFC1367B8A3CEF12729C00" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 1436 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP093240: gene expression differential - normal control versus hypertrophic cardiomyopathy (HCM): control; SRX2339810, SRX2339811, SRX2339812, SRX2339813: HCM; SRX2339805, SRX2339806, SRX2339807, SRX2339808, SRX2339809;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 9 variables:
## ..$ SRR5008356: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008357: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008358: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008359: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008360: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008361: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008362: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008363: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008364: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 9 variables:
## ..$ SRR5008356: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008357: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008358: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008359: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008360: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008361: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008362: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008363: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5008364: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 9 variables:
## ..$ SRR5008356: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR5008357: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR5008358: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR5008359: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR5008360: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR5008361: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR5008362: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR5008363: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## ..$ SRR5008364: chr [1:30] "SE" "Sanger/Illumina1.9" "49" "49" ...
## $ MetadataSummary:'data.frame': 9 obs. of 7 variables:
## ..$ QC_summary : chr [1:9] "WARN(5)" "WARN(5)" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:9] "SRX2339805" "SRX2339806" "SRX2339807" "SRX2339808" ...
## ..$ SRS_accession: chr [1:9] "SRS1794704" "SRS1794706" "SRS1794702" "SRS1794705" ...
## ..$ SRP_accession: chr [1:9] "SRP093240" "SRP093240" "SRP093240" "SRP093240" ...
## ..$ Sample_name : chr [1:9] "GSM2387228" "GSM2387229" "GSM2387230" "GSM2387231" ...
## ..$ GEO_series : chr [1:9] "GSE89714" "GSE89714" "GSE89714" "GSE89714" ...
## ..$ Library_name : logi [1:9] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 9 obs. of 52 variables:
## ..$ QC_summary : chr [1:9] "WARN(5)" "WARN(5)" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:9] "SRX2339805" "SRX2339806" "SRX2339807" "SRX2339808" ...
## ..$ SRS_accession : chr [1:9] "SRS1794704" "SRS1794706" "SRS1794702" "SRS1794705" ...
## ..$ SRP_accession : chr [1:9] "SRP093240" "SRP093240" "SRP093240" "SRP093240" ...
## ..$ Sample_name : chr [1:9] "GSM2387228" "GSM2387229" "GSM2387230" "GSM2387231" ...
## ..$ GEO_series : chr [1:9] "GSE89714" "GSE89714" "GSE89714" "GSE89714" ...
## ..$ Library_name : logi [1:9] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:9] "GSM2387228" "GSM2387229" "GSM2387230" "GSM2387231" ...
## ..$ ReleaseDate : chr [1:9] "2016-11-16 16:08:11" "2016-11-16 16:08:11" "2016-11-16 16:08:11" "2016-11-16 16:08:11" ...
## ..$ LoadDate : chr [1:9] "2016-11-09 15:02:29" "2016-11-09 15:02:19" "2016-11-09 15:02:22" "2016-11-09 15:02:14" ...
## ..$ spots : int [1:9] 14198589 14249976 14472554 15080712 14924562 14260478 14178862 14067628 14146943
## ..$ bases : int [1:9] 695730861 698248824 709155146 738954888 731303538 698763422 694764238 689313772 693200207
## ..$ spots_with_mates : int [1:9] 0 0 0 0 0 0 0 0 0
## ..$ avgLength : int [1:9] 49 49 49 49 49 49 49 49 49
## ..$ size_MB : int [1:9] 456 460 466 485 481 461 456 453 455
## ..$ AssemblyName : logi [1:9] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:9] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR5008356/SRR5008356.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5008357/SRR5008357.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5008358/SRR5008358.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5008359/SRR5008359.1" ...
## ..$ LibraryName : logi [1:9] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:9] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:9] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:9] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:9] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:9] 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:9] 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:9] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:9] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:9] "SRP093240" "SRP093240" "SRP093240" "SRP093240" ...
## ..$ BioProject : chr [1:9] "PRJNA352990" "PRJNA352990" "PRJNA352990" "PRJNA352990" ...
## ..$ Study_Pubmed_id : logi [1:9] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:9] 352990 352990 352990 352990 352990 352990 352990 352990 352990
## ..$ Sample : chr [1:9] "SRS1794704" "SRS1794706" "SRS1794702" "SRS1794705" ...
## ..$ BioSample : chr [1:9] "SAMN06007608" "SAMN06007634" "SAMN06007633" "SAMN06007632" ...
## ..$ SampleType : chr [1:9] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:9] 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:9] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:9] NA NA NA NA NA NA ...
## ..$ source : logi [1:9] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:9] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:9] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:9] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:9] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:9] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:9] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:9] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:9] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:9] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:9] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:9] "SRA492421" "SRA492421" "SRA492421" "SRA492421" ...
## ..$ dbgap_study_accession: logi [1:9] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:9] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:9] "CF61279888BA50C34D6D22A619C10B73" "462888B44B31C18015756CAF10A427CA" "FE055FEF4EA4D8A79F24A67046407556" "B0AD8119A5C231B95C669DA6CAFCE769" ...
## ..$ ReadHash : chr [1:9] "CE3D09F63B980D688E08AE0692825ECA" "1342736EDBF5030E82653407C98FD460" "018433AB5923BB986F96BF38FC232FC2" "C5DF62FDCE0DB88D88BADFCFC0586030" ...
## $ 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
## SRP026208:left ventricular control myocardial samples versus ischemic cardiomyopathy (ICM) sample: control; SRX312124, SRX312125, SRX312126, SRX312127, SRX312128, SRX312129, SRX312130, SRX312131, SRX312132, SRX312133, SRX312134, SRX312135, SRX312136, SRX312137, SRX312138, SRX312139: ICM samples; SRX312140, SRX312141, SRX312142, SRX312143, SRX312144, SRX312145, SRX3121246, SRX312147, SRX312148, SRX312149, SRX312150, SRX312151, SRX312152, SRX312153, SRX312154, SRX312155;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 22 variables:
## ..$ SRR915764: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915765: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915766: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915768: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915769: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915770: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915772: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR915773: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915774: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915775: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915776: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915777: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915780: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915781: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915783: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915784: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915785: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915788: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915790: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915792: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915793: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915794: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 22 variables:
## ..$ SRR915764: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915765: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915766: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915768: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915769: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915770: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915772: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915773: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915774: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915775: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915776: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915777: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915780: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915781: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915783: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915784: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915785: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915788: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915790: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915792: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915793: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR915794: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 22 variables:
## ..$ SRR915764: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915765: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915766: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915768: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915769: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915770: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915772: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915773: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915774: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915775: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915776: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915777: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915780: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915781: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915783: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915784: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915785: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915788: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915790: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915792: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915793: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR915794: chr [1:30] "PE" "Sanger/Illumina1.9" "36" "36" ...
## $ MetadataSummary:'data.frame': 22 obs. of 7 variables:
## ..$ QC_summary : chr [1:22] "FAIL(6)" "FAIL(6)" "FAIL(3,4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession: chr [1:22] "SRX312124" "SRX312125" "SRX312126" "SRX312128" ...
## ..$ SRS_accession: chr [1:22] "SRS449718" "SRS449719" "SRS449720" "SRS449721" ...
## ..$ SRP_accession: chr [1:22] "SRP026208" "SRP026208" "SRP026208" "SRP026208" ...
## ..$ Sample_name : chr [1:22] "GSM1171549" "GSM1171550" "GSM1171551" "GSM1171553" ...
## ..$ GEO_series : chr [1:22] "GSE48166" "GSE48166" "GSE48166" "GSE48166" ...
## ..$ Library_name : logi [1:22] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 22 obs. of 52 variables:
## ..$ QC_summary : chr [1:22] "FAIL(6)" "FAIL(6)" "FAIL(3,4,6)" "FAIL(3,4,6)" ...
## ..$ SRX_accession : chr [1:22] "SRX312124" "SRX312125" "SRX312126" "SRX312128" ...
## ..$ SRS_accession : chr [1:22] "SRS449718" "SRS449719" "SRS449720" "SRS449721" ...
## ..$ SRP_accession : chr [1:22] "SRP026208" "SRP026208" "SRP026208" "SRP026208" ...
## ..$ Sample_name : chr [1:22] "GSM1171549" "GSM1171550" "GSM1171551" "GSM1171553" ...
## ..$ GEO_series : chr [1:22] "GSE48166" "GSE48166" "GSE48166" "GSE48166" ...
## ..$ Library_name : logi [1:22] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:22] "GSM1171549" "GSM1171550" "GSM1171551" "GSM1171553" ...
## ..$ ReleaseDate : chr [1:22] "2015-07-22 17:04:43" "2015-07-22 17:04:43" "2015-07-22 17:04:43" "2015-07-22 17:04:44" ...
## ..$ LoadDate : chr [1:22] "2015-10-22 13:51:22" "2015-10-22 13:49:50" "2015-10-22 13:48:42" "2015-10-22 13:44:16" ...
## ..$ spots : int [1:22] 10385341 11203945 11045612 18732704 18361278 17662956 18404522 16431967 19088211 18330219 ...
## ..$ bases : int [1:22] 747744552 806684040 795284064 1348754688 1322012016 1271732832 1325125584 1183101624 1374351192 1319775768 ...
## ..$ spots_with_mates : int [1:22] 10385341 11203945 11045612 18732704 18361278 17662956 18404522 16431967 19088211 18330219 ...
## ..$ avgLength : int [1:22] 72 72 72 72 72 72 72 72 72 72 ...
## ..$ size_MB : int [1:22] 503 551 539 909 891 857 914 797 932 893 ...
## ..$ AssemblyName : logi [1:22] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:22] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR915764/SRR915764.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR915765/SRR915765.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR915766/SRR915766.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR915768/SRR915768.2" ...
## ..$ LibraryName : logi [1:22] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:22] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:22] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:22] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:22] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:22] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:22] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:22] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:22] "Illumina Genome Analyzer II" "Illumina Genome Analyzer II" "Illumina Genome Analyzer II" "Illumina Genome Analyzer II" ...
## ..$ SRAStudy : chr [1:22] "SRP026208" "SRP026208" "SRP026208" "SRP026208" ...
## ..$ BioProject : chr [1:22] "PRJNA209081" "PRJNA209081" "PRJNA209081" "PRJNA209081" ...
## ..$ Study_Pubmed_id : logi [1:22] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:22] 209081 209081 209081 209081 209081 209081 209081 209081 209081 209081 ...
## ..$ Sample : chr [1:22] "SRS449718" "SRS449719" "SRS449720" "SRS449721" ...
## ..$ BioSample : chr [1:22] "SAMN02209927" "SAMN02209928" "SAMN02209929" "SAMN02209930" ...
## ..$ SampleType : chr [1:22] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:22] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:22] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:22] NA NA NA NA NA NA ...
## ..$ source : logi [1:22] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:22] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:22] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:22] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:22] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:22] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:22] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:22] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:22] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:22] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:22] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:22] "SRA091408" "SRA091408" "SRA091408" "SRA091408" ...
## ..$ dbgap_study_accession: logi [1:22] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:22] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:22] "2F1464D596FEB74903BBF0C239B26B6C" "C208A41A135532A047FC971DA5E07CC2" "C2C8EC2391F0DFDDD479B5B1DA4C73B2" "F6BD2587E3799DDFEAA11ED44CE48129" ...
## ..$ ReadHash : chr [1:22] "C985D7458CF7D33955AF20E0770C79BB" "F93059CA8AF033BC9408291498521FF3" "EFB775F4E046877E742541AADF774A4C" "ABFD7A50BED0CB7A17E45DE6B592BCCA" ...
## $ absent : chr(0)## SRP188219:sinus rythm in left atrium versus right atrium:left atrium; SRX5509125, SRX5509127, SRX5509129, SRX5509131, SRX5509133:right atrium; SRX5509126, SRX5509128, SRX5509130, SRX5509132, SRX5509134; sex
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 1 variable:
## ..$ SRR8714875: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 1 variable:
## ..$ SRR8714875: 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 1 variable:
## ..$ SRR8714875: chr [1:30] "PE" "Sanger/Illumina1.9" "65" "76" ...
## $ MetadataSummary:'data.frame': 1 obs. of 7 variables:
## ..$ QC_summary : chr "WARN(1,5,7,8)"
## ..$ SRX_accession: chr "SRX5509126"
## ..$ SRS_accession: chr "SRS4477032"
## ..$ SRP_accession: chr "SRP188219"
## ..$ Sample_name : chr "GSM3666572"
## ..$ GEO_series : chr "GSE128188"
## ..$ Library_name : logi NA
## $ MetadataFull :'data.frame': 1 obs. of 52 variables:
## ..$ QC_summary : chr "WARN(1,5,7,8)"
## ..$ SRX_accession : chr "SRX5509126"
## ..$ SRS_accession : chr "SRS4477032"
## ..$ SRP_accession : chr "SRP188219"
## ..$ Sample_name : chr "GSM3666572"
## ..$ GEO_series : chr "GSE128188"
## ..$ Library_name : logi NA
## ..$ SampleName : chr "GSM3666572"
## ..$ ReleaseDate : chr "2019-03-13 19:13:18"
## ..$ LoadDate : chr "2019-03-12 13:50:28"
## ..$ spots : int 5866485
## ..$ bases : int 886052461
## ..$ spots_with_mates : int 5866485
## ..$ avgLength : int 151
## ..$ size_MB : int 330
## ..$ AssemblyName : logi NA
## ..$ download_path : chr "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR8714875/SRR8714875.1"
## ..$ LibraryName : logi NA
## ..$ LibraryStrategy : chr "RNA-Seq"
## ..$ LibrarySelection : chr "cDNA"
## ..$ LibrarySource : chr "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr "PAIRED"
## ..$ InsertSize : int 0
## ..$ InsertDev : num 0
## ..$ Platform : chr "ILLUMINA"
## ..$ Model : chr "NextSeq 500"
## ..$ SRAStudy : chr "SRP188219"
## ..$ BioProject : chr "PRJNA526687"
## ..$ Study_Pubmed_id : int 3
## ..$ ProjectID : int 526687
## ..$ Sample : chr "SRS4477032"
## ..$ BioSample : chr "SAMN11106952"
## ..$ SampleType : chr "simple"
## ..$ TaxID : int 9606
## ..$ ScientificName : chr "Homo sapiens"
## ..$ g1k_pop_code : logi NA
## ..$ source : logi NA
## ..$ g1k_analysis_group : logi NA
## ..$ Subject_ID : logi NA
## ..$ Sex : logi NA
## ..$ Disease : logi NA
## ..$ Tumor : chr "no"
## ..$ Affection_Status : logi NA
## ..$ Analyte_Type : logi NA
## ..$ Histological_Type : logi NA
## ..$ Body_Site : logi NA
## ..$ CenterName : chr "GEO"
## ..$ Submission : chr "SRA858970"
## ..$ dbgap_study_accession: logi NA
## ..$ Consent : chr "public"
## ..$ RunHash : chr "A4DF07CA4B73BC30DE5FF6DCBF2E04F6"
## ..$ ReadHash : chr "32DA805AEA944FC488B0B98E604AF427"
## $ absent : chr(0)## SRP188219:atrial fibrillation in left atrium versus right atrium:left atrium;SRX5509135, SRX5509137, SRX5509139, SRX5509141, SRX5509143:right atrium; SRX5509136, SRX5509138, SRX5509140, SRX5509142, SRX5509144; sex## Error. None of the specified SRR accessions are present.## NULL## SRP188219: sinus rythm in the left atrium versus atrial fibrilation in the left atrium:sinus rythm; SRX5509127, SRX5509129, SRX5509131, SRX5509132, SRX5509133:atrial fibrillation; SRX5509135, SRX5509137, SRX5509139, SRX5509141, SRX5509142; sex
## Error. None of the specified SRR accessions are present.## NULL## SRP188219:sinus rythm in the right atrium versus atrial fibrilation in the right atrium: sinus rythm; SRX5509126, SRX5509128, SRX5509130, SRX5509132, SRX5509134:atrial fibrillation; SRX5509136, SRX5509138, SRX5509140, SRX5509141, SRX5509142; sex## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 1 variable:
## ..$ SRR8714875: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 1 variable:
## ..$ SRR8714875: 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 1 variable:
## ..$ SRR8714875: chr [1:30] "PE" "Sanger/Illumina1.9" "65" "76" ...
## $ MetadataSummary:'data.frame': 1 obs. of 7 variables:
## ..$ QC_summary : chr "WARN(1,5,7,8)"
## ..$ SRX_accession: chr "SRX5509126"
## ..$ SRS_accession: chr "SRS4477032"
## ..$ SRP_accession: chr "SRP188219"
## ..$ Sample_name : chr "GSM3666572"
## ..$ GEO_series : chr "GSE128188"
## ..$ Library_name : logi NA
## $ MetadataFull :'data.frame': 1 obs. of 52 variables:
## ..$ QC_summary : chr "WARN(1,5,7,8)"
## ..$ SRX_accession : chr "SRX5509126"
## ..$ SRS_accession : chr "SRS4477032"
## ..$ SRP_accession : chr "SRP188219"
## ..$ Sample_name : chr "GSM3666572"
## ..$ GEO_series : chr "GSE128188"
## ..$ Library_name : logi NA
## ..$ SampleName : chr "GSM3666572"
## ..$ ReleaseDate : chr "2019-03-13 19:13:18"
## ..$ LoadDate : chr "2019-03-12 13:50:28"
## ..$ spots : int 5866485
## ..$ bases : int 886052461
## ..$ spots_with_mates : int 5866485
## ..$ avgLength : int 151
## ..$ size_MB : int 330
## ..$ AssemblyName : logi NA
## ..$ download_path : chr "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR8714875/SRR8714875.1"
## ..$ LibraryName : logi NA
## ..$ LibraryStrategy : chr "RNA-Seq"
## ..$ LibrarySelection : chr "cDNA"
## ..$ LibrarySource : chr "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr "PAIRED"
## ..$ InsertSize : int 0
## ..$ InsertDev : num 0
## ..$ Platform : chr "ILLUMINA"
## ..$ Model : chr "NextSeq 500"
## ..$ SRAStudy : chr "SRP188219"
## ..$ BioProject : chr "PRJNA526687"
## ..$ Study_Pubmed_id : int 3
## ..$ ProjectID : int 526687
## ..$ Sample : chr "SRS4477032"
## ..$ BioSample : chr "SAMN11106952"
## ..$ SampleType : chr "simple"
## ..$ TaxID : int 9606
## ..$ ScientificName : chr "Homo sapiens"
## ..$ g1k_pop_code : logi NA
## ..$ source : logi NA
## ..$ g1k_analysis_group : logi NA
## ..$ Subject_ID : logi NA
## ..$ Sex : logi NA
## ..$ Disease : logi NA
## ..$ Tumor : chr "no"
## ..$ Affection_Status : logi NA
## ..$ Analyte_Type : logi NA
## ..$ Histological_Type : logi NA
## ..$ Body_Site : logi NA
## ..$ CenterName : chr "GEO"
## ..$ Submission : chr "SRA858970"
## ..$ dbgap_study_accession: logi NA
## ..$ Consent : chr "public"
## ..$ RunHash : chr "A4DF07CA4B73BC30DE5FF6DCBF2E04F6"
## ..$ ReadHash : chr "32DA805AEA944FC488B0B98E604AF427"
## $ absent : chr(0)## SRP021193: non-failing (NF) in left ventricle apex tissue versus ischemic cardiomyopathy (ICM) using RNASeq:NF; SRX268708, SRX268709, SRX268710, SRX268711, SRX268712, SRX268713, SRX268714, SRX268715:ICM; SRX268716, SRX268717, SRX268718, SRX268719, SRX268720, SRX268721, SRX268722, SRX268723; LVAD support
## 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:
## ..$ SRR830965: int [1:58302] 0 15 0 0 0 0 0 0 0 0 ...
## ..$ SRR830966: int [1:58302] 1 12 3 1 0 0 0 0 0 0 ...
## ..$ SRR830967: int [1:58302] 0 10 0 0 0 0 0 0 0 0 ...
## ..$ SRR830968: int [1:58302] 0 6 1 0 0 0 0 0 0 0 ...
## ..$ SRR830969: int [1:58302] 0 18 2 1 0 0 0 0 0 0 ...
## ..$ SRR830970: int [1:58302] 0 16 1 0 0 0 0 0 0 0 ...
## ..$ SRR830971: int [1:58302] 0 26 3 0 0 0 0 0 0 0 ...
## ..$ SRR830972: int [1:58302] 0 13 1 0 0 0 0 0 0 0 ...
## ..$ SRR830973: int [1:58302] 0 14 2 0 0 0 0 0 1 7 ...
## ..$ SRR830974: int [1:58302] 0 7 3 0 0 0 0 0 0 0 ...
## ..$ SRR830975: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR830976: int [1:58302] 0 18 4 0 0 0 0 0 0 1 ...
## ..$ SRR830977: int [1:58302] 0 16 0 0 0 0 0 0 0 1 ...
## ..$ SRR830978: int [1:58302] 0 14 0 0 0 0 0 0 0 1 ...
## ..$ SRR830979: int [1:58302] 0 24 5 0 0 0 0 0 0 0 ...
## ..$ SRR830980: int [1:58302] 0 19 3 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 16 variables:
## ..$ SRR830965: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830966: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830967: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830968: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830969: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830970: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830971: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830972: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830973: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830974: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830975: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830976: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830977: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830978: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830980: 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:
## ..$ SRR830965: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830966: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830967: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830968: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830969: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830970: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830971: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830972: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830973: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830974: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830975: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830976: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830977: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830978: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830979: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830980: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 16 obs. of 7 variables:
## ..$ QC_summary : chr [1:16] "WARN(1,5,7)" "PASS" "WARN(5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:16] "SRX268708" "SRX268709" "SRX268710" "SRX268711" ...
## ..$ SRS_accession: chr [1:16] "SRS414574" "SRS414575" "SRS414576" "SRS414577" ...
## ..$ SRP_accession: chr [1:16] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ Sample_name : chr [1:16] "GSM1126612" "GSM1126613" "GSM1126614" "GSM1126615" ...
## ..$ GEO_series : chr [1:16] "GSE46224" "GSE46224" "GSE46224" "GSE46224" ...
## ..$ 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)" "PASS" "WARN(5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:16] "SRX268708" "SRX268709" "SRX268710" "SRX268711" ...
## ..$ SRS_accession : chr [1:16] "SRS414574" "SRS414575" "SRS414576" "SRS414577" ...
## ..$ SRP_accession : chr [1:16] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ Sample_name : chr [1:16] "GSM1126612" "GSM1126613" "GSM1126614" "GSM1126615" ...
## ..$ GEO_series : chr [1:16] "GSE46224" "GSE46224" "GSE46224" "GSE46224" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:16] "GSM1126612" "GSM1126613" "GSM1126614" "GSM1126615" ...
## ..$ ReleaseDate : chr [1:16] "2015-07-22 17:03:54" "2015-07-22 17:03:54" "2015-07-22 17:03:57" "2015-07-22 17:03:57" ...
## ..$ LoadDate : chr [1:16] "2015-11-11 17:18:08" "2015-11-11 17:21:00" "2015-11-11 17:10:45" "2015-11-11 17:07:18" ...
## ..$ spots : int [1:16] 8323741 19020427 10468556 9682901 11502860 12373149 20311731 20398217 23914383 15142110 ...
## ..$ bases : num [1:16] 1.68e+09 3.84e+09 2.11e+09 1.96e+09 2.32e+09 ...
## ..$ spots_with_mates : int [1:16] 8323741 19020427 10468556 9682901 11502860 12373149 20311731 20398217 23914383 15142110 ...
## ..$ avgLength : int [1:16] 202 202 202 202 202 202 202 202 202 202 ...
## ..$ size_MB : int [1:16] 1098 2529 1214 1121 1407 1517 2669 2665 3176 1990 ...
## ..$ AssemblyName : logi [1:16] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:16] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830965/SRR830965.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830966/SRR830966.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830967/SRR830967.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830968/SRR830968.2" ...
## ..$ LibraryName : logi [1:16] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:16] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:16] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:16] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:16] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:16] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:16] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:16] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ BioProject : chr [1:16] "PRJNA198165" "PRJNA198165" "PRJNA198165" "PRJNA198165" ...
## ..$ Study_Pubmed_id : int [1:16] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:16] 198165 198165 198165 198165 198165 198165 198165 198165 198165 198165 ...
## ..$ Sample : chr [1:16] "SRS414574" "SRS414575" "SRS414576" "SRS414577" ...
## ..$ BioSample : chr [1:16] "SAMN02053683" "SAMN02053684" "SAMN02053685" "SAMN02053686" ...
## ..$ 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] "SRA073740" "SRA073740" "SRA073740" "SRA073740" ...
## ..$ dbgap_study_accession: logi [1:16] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:16] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:16] "3169106D02B317CE2A40100FE4DB9E53" "C051C1B2D6F577A4585FECC2FE6AE748" "A0F339D89D14D68F94D695B63F5C6215" "6483286689170A8EF26525CD1F2CF894" ...
## ..$ ReadHash : chr [1:16] "03BC51519E91AFD17C948F35F1C05491" "803E0FC7DC0C97A21C54254F299693C5" "D7669B522588FEA696282D41C0881719" "1ADE7B419A5AFF49AD39E0A2CDF0B522" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 60 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP021193: non-failing (NF) in left ventricle apex tissue versus non-ischemic cardiomyopathy (NICM) using RNASeq:NF; SRX268708, SRX268709, SRX268710, SRX268711, SRX268712, SRX268713, SRX268714, SRX268715:NICM; SRX268724, SRX268725, SRX268726, SRX268727, SRX268728, SRX268729, SRX268730, SRX268731; LVAD support## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR830965: int [1:58302] 0 15 0 0 0 0 0 0 0 0 ...
## ..$ SRR830966: int [1:58302] 1 12 3 1 0 0 0 0 0 0 ...
## ..$ SRR830967: int [1:58302] 0 10 0 0 0 0 0 0 0 0 ...
## ..$ SRR830968: int [1:58302] 0 6 1 0 0 0 0 0 0 0 ...
## ..$ SRR830969: int [1:58302] 0 18 2 1 0 0 0 0 0 0 ...
## ..$ SRR830970: int [1:58302] 0 16 1 0 0 0 0 0 0 0 ...
## ..$ SRR830971: int [1:58302] 0 26 3 0 0 0 0 0 0 0 ...
## ..$ SRR830972: int [1:58302] 0 13 1 0 0 0 0 0 0 0 ...
## ..$ SRR830981: int [1:58302] 0 7 0 0 0 0 0 0 0 3 ...
## ..$ SRR830982: int [1:58302] 0 5 0 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR830965: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830966: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830967: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830968: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830969: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830970: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830971: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830972: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830982: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR830965: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830966: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830967: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830968: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830969: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830970: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830971: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830972: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830981: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830982: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "WARN(1,5,7)" "PASS" "WARN(5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession: chr [1:10] "SRX268708" "SRX268709" "SRX268710" "SRX268711" ...
## ..$ SRS_accession: chr [1:10] "SRS414574" "SRS414575" "SRS414576" "SRS414577" ...
## ..$ SRP_accession: chr [1:10] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ Sample_name : chr [1:10] "GSM1126612" "GSM1126613" "GSM1126614" "GSM1126615" ...
## ..$ GEO_series : chr [1:10] "GSE46224" "GSE46224" "GSE46224" "GSE46224" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "WARN(1,5,7)" "PASS" "WARN(5,7)" "WARN(1,5,7)" ...
## ..$ SRX_accession : chr [1:10] "SRX268708" "SRX268709" "SRX268710" "SRX268711" ...
## ..$ SRS_accession : chr [1:10] "SRS414574" "SRS414575" "SRS414576" "SRS414577" ...
## ..$ SRP_accession : chr [1:10] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ Sample_name : chr [1:10] "GSM1126612" "GSM1126613" "GSM1126614" "GSM1126615" ...
## ..$ GEO_series : chr [1:10] "GSE46224" "GSE46224" "GSE46224" "GSE46224" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM1126612" "GSM1126613" "GSM1126614" "GSM1126615" ...
## ..$ ReleaseDate : chr [1:10] "2015-07-22 17:03:54" "2015-07-22 17:03:54" "2015-07-22 17:03:57" "2015-07-22 17:03:57" ...
## ..$ LoadDate : chr [1:10] "2015-11-11 17:18:08" "2015-11-11 17:21:00" "2015-11-11 17:10:45" "2015-11-11 17:07:18" ...
## ..$ spots : int [1:10] 8323741 19020427 10468556 9682901 11502860 12373149 20311731 20398217 10497039 12847919
## ..$ bases : num [1:10] 1.68e+09 3.84e+09 2.11e+09 1.96e+09 2.32e+09 ...
## ..$ spots_with_mates : int [1:10] 8323741 19020427 10468556 9682901 11502860 12373149 20311731 20398217 10497039 12847919
## ..$ avgLength : int [1:10] 202 202 202 202 202 202 202 202 202 202
## ..$ size_MB : int [1:10] 1098 2529 1214 1121 1407 1517 2669 2665 1390 1730
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830965/SRR830965.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830966/SRR830966.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830967/SRR830967.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830968/SRR830968.2" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:10] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ BioProject : chr [1:10] "PRJNA198165" "PRJNA198165" "PRJNA198165" "PRJNA198165" ...
## ..$ Study_Pubmed_id : int [1:10] 2 2 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:10] 198165 198165 198165 198165 198165 198165 198165 198165 198165 198165
## ..$ Sample : chr [1:10] "SRS414574" "SRS414575" "SRS414576" "SRS414577" ...
## ..$ BioSample : chr [1:10] "SAMN02053683" "SAMN02053684" "SAMN02053685" "SAMN02053686" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA073740" "SRA073740" "SRA073740" "SRA073740" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "3169106D02B317CE2A40100FE4DB9E53" "C051C1B2D6F577A4585FECC2FE6AE748" "A0F339D89D14D68F94D695B63F5C6215" "6483286689170A8EF26525CD1F2CF894" ...
## ..$ ReadHash : chr [1:10] "03BC51519E91AFD17C948F35F1C05491" "803E0FC7DC0C97A21C54254F299693C5" "D7669B522588FEA696282D41C0881719" "1ADE7B419A5AFF49AD39E0A2CDF0B522" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 91 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP021193: ischemic cardiomyopathy (ICM) versus non-ischemic cardiomyopathy (NICM) using RNASeq:ICM; SRX268716, SRX268717, SRX268718, SRX268719, SRX268720, SRX268721, SRX268722, SRX268723:NICM; SRX268724, SRX268725, SRX268726, SRX268727, SRX268728, SRX268729, SRX268730, SRX268731; LVAD support## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 10 variables:
## ..$ SRR830973: int [1:58302] 0 14 2 0 0 0 0 0 1 7 ...
## ..$ SRR830974: int [1:58302] 0 7 3 0 0 0 0 0 0 0 ...
## ..$ SRR830975: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR830976: int [1:58302] 0 18 4 0 0 0 0 0 0 1 ...
## ..$ SRR830977: int [1:58302] 0 16 0 0 0 0 0 0 0 1 ...
## ..$ SRR830978: int [1:58302] 0 14 0 0 0 0 0 0 0 1 ...
## ..$ SRR830979: int [1:58302] 0 24 5 0 0 0 0 0 0 0 ...
## ..$ SRR830980: int [1:58302] 0 19 3 0 0 0 0 0 0 0 ...
## ..$ SRR830981: int [1:58302] 0 7 0 0 0 0 0 0 0 3 ...
## ..$ SRR830982: int [1:58302] 0 5 0 0 0 0 0 0 0 1 ...
## $ TxCounts :'data.frame': 180869 obs. of 10 variables:
## ..$ SRR830973: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830974: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830975: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830976: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830977: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830978: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830982: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 10 variables:
## ..$ SRR830973: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830974: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830975: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830976: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830977: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830978: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830979: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830980: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830981: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830982: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 10 obs. of 7 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "WARN(1,5,7)" "PASS" ...
## ..$ SRX_accession: chr [1:10] "SRX268716" "SRX268717" "SRX268718" "SRX268719" ...
## ..$ SRS_accession: chr [1:10] "SRS414528" "SRS414529" "SRS414530" "SRS414531" ...
## ..$ SRP_accession: chr [1:10] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ Sample_name : chr [1:10] "GSM1126620" "GSM1126621" "GSM1126622" "GSM1126623" ...
## ..$ GEO_series : chr [1:10] "GSE46224" "GSE46224" "GSE46224" "GSE46224" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 10 obs. of 52 variables:
## ..$ QC_summary : chr [1:10] "PASS" "PASS" "WARN(1,5,7)" "PASS" ...
## ..$ SRX_accession : chr [1:10] "SRX268716" "SRX268717" "SRX268718" "SRX268719" ...
## ..$ SRS_accession : chr [1:10] "SRS414528" "SRS414529" "SRS414530" "SRS414531" ...
## ..$ SRP_accession : chr [1:10] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ Sample_name : chr [1:10] "GSM1126620" "GSM1126621" "GSM1126622" "GSM1126623" ...
## ..$ GEO_series : chr [1:10] "GSE46224" "GSE46224" "GSE46224" "GSE46224" ...
## ..$ Library_name : logi [1:10] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:10] "GSM1126620" "GSM1126621" "GSM1126622" "GSM1126623" ...
## ..$ ReleaseDate : chr [1:10] "2015-07-22 17:03:58" "2015-07-22 17:03:58" "2015-07-22 17:03:58" "2015-07-22 17:03:58" ...
## ..$ LoadDate : chr [1:10] "2015-11-11 17:00:50" "2015-11-11 16:43:24" "2015-11-11 16:37:24" "2015-11-11 16:35:53" ...
## ..$ spots : int [1:10] 23914383 15142110 9010915 19088790 9939298 9179777 18869689 18075404 10497039 12847919
## ..$ bases : num [1:10] 4.83e+09 3.06e+09 1.82e+09 3.86e+09 2.01e+09 ...
## ..$ spots_with_mates : int [1:10] 23914383 15142110 9010915 19088790 9939298 9179777 18869689 18075404 10497039 12847919
## ..$ avgLength : int [1:10] 202 202 202 202 202 202 202 202 202 202
## ..$ size_MB : int [1:10] 3176 1990 1046 2232 1206 1119 2469 2363 1390 1730
## ..$ AssemblyName : logi [1:10] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:10] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830973/SRR830973.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830974/SRR830974.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830975/SRR830975.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830976/SRR830976.2" ...
## ..$ LibraryName : logi [1:10] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:10] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:10] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:10] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:10] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:10] 0 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:10] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:10] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:10] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ BioProject : chr [1:10] "PRJNA198165" "PRJNA198165" "PRJNA198165" "PRJNA198165" ...
## ..$ Study_Pubmed_id : int [1:10] 2 2 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:10] 198165 198165 198165 198165 198165 198165 198165 198165 198165 198165
## ..$ Sample : chr [1:10] "SRS414528" "SRS414529" "SRS414530" "SRS414531" ...
## ..$ BioSample : chr [1:10] "SAMN02053691" "SAMN02053692" "SAMN02053693" "SAMN02053694" ...
## ..$ SampleType : chr [1:10] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:10] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:10] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:10] NA NA NA NA NA NA ...
## ..$ source : logi [1:10] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:10] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:10] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:10] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:10] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:10] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:10] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:10] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:10] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:10] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:10] "SRA073740" "SRA073740" "SRA073740" "SRA073740" ...
## ..$ dbgap_study_accession: logi [1:10] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:10] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:10] "F6CA50D6696A6B27D55747B6EEC571CD" "C05A8181C5D53AAED8B4B32DB4784501" "E22E817D5C12D4173CA043BE3DFE5983" "CD97B4B43C890CFFDF60E343527D135F" ...
## ..$ ReadHash : chr [1:10] "5B3836BCB96FB61CE4DC64C625ECC9D5" "4C6073AB1F43E297BD8EBCE9CF1027C3" "F5E95DADB38BA4B9F59FA299D4EA76BE" "44219326AF2D7D2FA6AC26798D2E9A71" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 73 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP021193:ischemic cardiomyopathy (ICM) versus ischemic cardiomyopathy post left ventricular assist device (ICM+LVAD):ICM; SRX268716, SRX268717, SRX268718, SRX268719, SRX268720, SRX268721, SRX268722, SRX268723:ICM+LVAD; SRX268732, SRX268733, SRX268734, SRX268735, SRX268736, SRX268737, SRX268738, SRX268739; LVAD support## 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:
## ..$ SRR830973: int [1:58302] 0 14 2 0 0 0 0 0 1 7 ...
## ..$ SRR830974: int [1:58302] 0 7 3 0 0 0 0 0 0 0 ...
## ..$ SRR830975: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR830976: int [1:58302] 0 18 4 0 0 0 0 0 0 1 ...
## ..$ SRR830977: int [1:58302] 0 16 0 0 0 0 0 0 0 1 ...
## ..$ SRR830978: int [1:58302] 0 14 0 0 0 0 0 0 0 1 ...
## ..$ SRR830979: int [1:58302] 0 24 5 0 0 0 0 0 0 0 ...
## ..$ SRR830980: int [1:58302] 0 19 3 0 0 0 0 0 0 0 ...
## ..$ SRR830989: int [1:58302] 0 21 4 1 0 0 0 0 0 1 ...
## ..$ SRR830990: int [1:58302] 0 8 1 0 0 0 0 0 0 0 ...
## ..$ SRR830991: int [1:58302] 0 4 0 0 0 0 0 0 0 0 ...
## ..$ SRR830992: int [1:58302] 0 3 1 1 0 0 0 0 0 0 ...
## ..$ SRR830993: int [1:58302] 0 18 0 0 0 0 0 0 0 0 ...
## ..$ SRR830994: int [1:58302] 0 26 1 0 0 0 0 0 0 0 ...
## ..$ SRR830995: int [1:58302] 0 18 3 0 0 0 0 0 0 1 ...
## ..$ SRR830996: int [1:58302] 0 16 6 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 16 variables:
## ..$ SRR830973: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830974: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830975: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830976: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830977: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830978: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830989: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830990: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830991: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830992: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830993: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830994: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830995: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830996: 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:
## ..$ SRR830973: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830974: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830975: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830976: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830977: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830978: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830979: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830980: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830989: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830990: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830991: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830992: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830993: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830994: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830995: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830996: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 16 obs. of 7 variables:
## ..$ QC_summary : chr [1:16] "PASS" "PASS" "WARN(1,5,7)" "PASS" ...
## ..$ SRX_accession: chr [1:16] "SRX268716" "SRX268717" "SRX268718" "SRX268719" ...
## ..$ SRS_accession: chr [1:16] "SRS414528" "SRS414529" "SRS414530" "SRS414531" ...
## ..$ SRP_accession: chr [1:16] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ Sample_name : chr [1:16] "GSM1126620" "GSM1126621" "GSM1126622" "GSM1126623" ...
## ..$ GEO_series : chr [1:16] "GSE46224" "GSE46224" "GSE46224" "GSE46224" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 16 obs. of 52 variables:
## ..$ QC_summary : chr [1:16] "PASS" "PASS" "WARN(1,5,7)" "PASS" ...
## ..$ SRX_accession : chr [1:16] "SRX268716" "SRX268717" "SRX268718" "SRX268719" ...
## ..$ SRS_accession : chr [1:16] "SRS414528" "SRS414529" "SRS414530" "SRS414531" ...
## ..$ SRP_accession : chr [1:16] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ Sample_name : chr [1:16] "GSM1126620" "GSM1126621" "GSM1126622" "GSM1126623" ...
## ..$ GEO_series : chr [1:16] "GSE46224" "GSE46224" "GSE46224" "GSE46224" ...
## ..$ Library_name : logi [1:16] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:16] "GSM1126620" "GSM1126621" "GSM1126622" "GSM1126623" ...
## ..$ ReleaseDate : chr [1:16] "2015-07-22 17:03:58" "2015-07-22 17:03:58" "2015-07-22 17:03:58" "2015-07-22 17:03:58" ...
## ..$ LoadDate : chr [1:16] "2015-11-11 17:00:50" "2015-11-11 16:43:24" "2015-11-11 16:37:24" "2015-11-11 16:35:53" ...
## ..$ spots : int [1:16] 23914383 15142110 9010915 19088790 9939298 9179777 18869689 18075404 16858952 9410533 ...
## ..$ bases : num [1:16] 4.83e+09 3.06e+09 1.82e+09 3.86e+09 2.01e+09 ...
## ..$ spots_with_mates : int [1:16] 23914383 15142110 9010915 19088790 9939298 9179777 18869689 18075404 16858952 9410533 ...
## ..$ avgLength : int [1:16] 202 202 202 202 202 202 202 202 202 202 ...
## ..$ size_MB : int [1:16] 3176 1990 1046 2232 1206 1119 2469 2363 2228 1252 ...
## ..$ AssemblyName : logi [1:16] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:16] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830973/SRR830973.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830974/SRR830974.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830975/SRR830975.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830976/SRR830976.2" ...
## ..$ LibraryName : logi [1:16] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:16] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:16] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:16] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:16] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:16] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:16] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:16] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:16] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ BioProject : chr [1:16] "PRJNA198165" "PRJNA198165" "PRJNA198165" "PRJNA198165" ...
## ..$ Study_Pubmed_id : int [1:16] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:16] 198165 198165 198165 198165 198165 198165 198165 198165 198165 198165 ...
## ..$ Sample : chr [1:16] "SRS414528" "SRS414529" "SRS414530" "SRS414531" ...
## ..$ BioSample : chr [1:16] "SAMN02053691" "SAMN02053692" "SAMN02053693" "SAMN02053694" ...
## ..$ 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] "SRA073740" "SRA073740" "SRA073740" "SRA073740" ...
## ..$ dbgap_study_accession: logi [1:16] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:16] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:16] "F6CA50D6696A6B27D55747B6EEC571CD" "C05A8181C5D53AAED8B4B32DB4784501" "E22E817D5C12D4173CA043BE3DFE5983" "CD97B4B43C890CFFDF60E343527D135F" ...
## ..$ ReadHash : chr [1:16] "5B3836BCB96FB61CE4DC64C625ECC9D5" "4C6073AB1F43E297BD8EBCE9CF1027C3" "F5E95DADB38BA4B9F59FA299D4EA76BE" "44219326AF2D7D2FA6AC26798D2E9A71" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 39 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP021193:non-ischemic cardiomyopathy(NICM) versus non-ischemic cardiomyopathy post left ventricular assist device (NICM+LVAD):NICM; SRX268724, SRX268725, SRX268726, SRX268727, SRX268728, SRX268729, SRX268730, SRX268731:NICM+LVAD; SRX268740, SRX268741,SRX268742, SRX268743, SRX268744, SRX268745, SRX268746, SRX268747## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 9 variables:
## ..$ SRR830981: int [1:58302] 0 7 0 0 0 0 0 0 0 3 ...
## ..$ SRR830982: int [1:58302] 0 5 0 0 0 0 0 0 0 1 ...
## ..$ SRR830997: int [1:58302] 0 15 0 0 0 0 0 0 0 1 ...
## ..$ SRR830998: int [1:58302] 0 20 7 0 0 0 0 0 0 0 ...
## ..$ SRR830999: int [1:58302] 0 9 2 0 0 0 0 0 0 0 ...
## ..$ SRR831000: int [1:58302] 0 5 0 0 0 0 0 0 0 1 ...
## ..$ SRR831001: int [1:58302] 1 36 2 0 0 0 0 0 0 0 ...
## ..$ SRR831002: int [1:58302] 0 19 0 0 0 0 0 0 0 0 ...
## ..$ SRR831003: int [1:58302] 0 22 2 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 9 variables:
## ..$ SRR830981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830982: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830997: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830998: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR830999: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR831000: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR831001: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR831002: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR831003: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 9 variables:
## ..$ SRR830981: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830982: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830997: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830998: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR830999: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR831000: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR831001: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR831002: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR831003: chr [1:30] "PE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 9 obs. of 7 variables:
## ..$ QC_summary : chr [1:9] "WARN(5,7)" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:9] "SRX268724" "SRX268725" "SRX268740" "SRX268741" ...
## ..$ SRS_accession: chr [1:9] "SRS414537" "SRS414536" "SRS414594" "SRS414595" ...
## ..$ SRP_accession: chr [1:9] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ Sample_name : chr [1:9] "GSM1126628" "GSM1126629" "GSM1126644" "GSM1126645" ...
## ..$ GEO_series : chr [1:9] "GSE46224" "GSE46224" "GSE46224" "GSE46224" ...
## ..$ Library_name : logi [1:9] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 9 obs. of 52 variables:
## ..$ QC_summary : chr [1:9] "WARN(5,7)" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:9] "SRX268724" "SRX268725" "SRX268740" "SRX268741" ...
## ..$ SRS_accession : chr [1:9] "SRS414537" "SRS414536" "SRS414594" "SRS414595" ...
## ..$ SRP_accession : chr [1:9] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ Sample_name : chr [1:9] "GSM1126628" "GSM1126629" "GSM1126644" "GSM1126645" ...
## ..$ GEO_series : chr [1:9] "GSE46224" "GSE46224" "GSE46224" "GSE46224" ...
## ..$ Library_name : logi [1:9] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:9] "GSM1126628" "GSM1126629" "GSM1126644" "GSM1126645" ...
## ..$ ReleaseDate : chr [1:9] "2015-07-22 17:03:54" "2015-07-22 17:03:54" "2015-07-22 17:03:55" "2015-07-22 17:03:54" ...
## ..$ LoadDate : chr [1:9] "2015-11-11 16:09:33" "2015-11-11 16:08:24" "2015-11-11 15:05:31" "2015-11-11 15:02:31" ...
## ..$ spots : int [1:9] 10497039 12847919 16738674 20252252 9604027 14660420 13666318 12405186 19029934
## ..$ bases : num [1:9] 2.12e+09 2.60e+09 3.38e+09 4.09e+09 1.94e+09 ...
## ..$ spots_with_mates : int [1:9] 10497039 12847919 16738674 20252252 9604027 14660420 13666318 12405186 19029934
## ..$ avgLength : int [1:9] 202 202 202 202 202 202 202 202 202
## ..$ size_MB : int [1:9] 1390 1730 2198 2725 1112 1697 1662 1529 2491
## ..$ AssemblyName : logi [1:9] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:9] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830981/SRR830981.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830982/SRR830982.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830997/SRR830997.2" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR830998/SRR830998.2" ...
## ..$ LibraryName : logi [1:9] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:9] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:9] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:9] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:9] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:9] 0 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:9] 0 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:9] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:9] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:9] "SRP021193" "SRP021193" "SRP021193" "SRP021193" ...
## ..$ BioProject : chr [1:9] "PRJNA198165" "PRJNA198165" "PRJNA198165" "PRJNA198165" ...
## ..$ Study_Pubmed_id : int [1:9] 2 2 2 2 2 2 2 2 2
## ..$ ProjectID : int [1:9] 198165 198165 198165 198165 198165 198165 198165 198165 198165
## ..$ Sample : chr [1:9] "SRS414537" "SRS414536" "SRS414594" "SRS414595" ...
## ..$ BioSample : chr [1:9] "SAMN02053699" "SAMN02053700" "SAMN02053723" "SAMN02053724" ...
## ..$ SampleType : chr [1:9] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:9] 9606 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:9] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:9] NA NA NA NA NA NA ...
## ..$ source : logi [1:9] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:9] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:9] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:9] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:9] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:9] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:9] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:9] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:9] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:9] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:9] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:9] "SRA073740" "SRA073740" "SRA073740" "SRA073740" ...
## ..$ dbgap_study_accession: logi [1:9] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:9] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:9] "D27E048B3817994DE46D101B254A2337" "0DAB5A37ABE654A1C053F6EC3AD5BA7C" "8D6C533EB6B6092E505D8D1F1D54206C" "5F5065D61770DC92EF53C78A2EEF6420" ...
## ..$ ReadHash : chr [1:9] "2590898AF674C05CB38AD2BCCFD7BD17" "9E314B211C676EE25A8833BA16B0036B" "389B5B1D11E846A16D4A9F3B118A472C" "EC3F49CF2031023B6858418E2A973375" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 214 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP166274:human induced pluripotent stem cell-derived cardiomyocytes from a familial control versus cardiomyopathy:familial control; SRX4910761, SRX4910762, SRX4910763: cardiomyopathy; SRX4910764, SRX4910765, SRX4910766; paired;## Error. None of the specified SRR accessions are present.## NULL## SRP163478: right ventricle of non-failing control versus right ventricle of left ventricular heart failure (LV-HF): control; SRX4799399, SRX4799401, SRX4799402, SRX4799403, SRX4799404: LV-HF; SRX4799404, SRX4799405, SRX4799406, SRX4799407, SRX4799408;## SRP163478: right ventricle of non-failing control versus right ventricle of biventricular heart failure (BiV-HF): control; SRX4799399, SRX4799401, SRX4799402, SRX4799403, SRX4799404: BiV-HF; SRX4799409, SRX4799410, SRX4799411, SRX4799412, SRX4799413;## 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:
## ..$ SRR7965778: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965780: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965781: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965787: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965788: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965789: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR7965778: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965780: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965781: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965787: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965788: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965789: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR7965778: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965780: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965781: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965787: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965788: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965789: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(5,7)" "WARN(5,7)" "WARN(5,7)" "WARN(5,7)" ...
## ..$ SRX_accession: chr [1:6] "SRX4799401" "SRX4799403" "SRX4799404" "SRX4799410" ...
## ..$ SRS_accession: chr [1:6] "SRS3878457" "SRS3878459" "SRS3878460" "SRS3878466" ...
## ..$ SRP_accession: chr [1:6] "SRP163478" "SRP163478" "SRP163478" "SRP163478" ...
## ..$ Sample_name : chr [1:6] "GSM3417068" "GSM3417070" "GSM3417071" "GSM3417077" ...
## ..$ GEO_series : chr [1:6] "GSE120852" "GSE120852" "GSE120852" "GSE120852" ...
## ..$ 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)" "WARN(5,7)" "WARN(5,7)" "WARN(5,7)" ...
## ..$ SRX_accession : chr [1:6] "SRX4799401" "SRX4799403" "SRX4799404" "SRX4799410" ...
## ..$ SRS_accession : chr [1:6] "SRS3878457" "SRS3878459" "SRS3878460" "SRS3878466" ...
## ..$ SRP_accession : chr [1:6] "SRP163478" "SRP163478" "SRP163478" "SRP163478" ...
## ..$ Sample_name : chr [1:6] "GSM3417068" "GSM3417070" "GSM3417071" "GSM3417077" ...
## ..$ GEO_series : chr [1:6] "GSE120852" "GSE120852" "GSE120852" "GSE120852" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM3417068" "GSM3417070" "GSM3417071" "GSM3417077" ...
## ..$ ReleaseDate : chr [1:6] "2018-10-08 18:32:08" "2018-10-08 18:32:08" "2018-10-08 18:32:08" "2018-10-08 18:32:08" ...
## ..$ LoadDate : chr [1:6] "2018-10-04 16:48:49" "2018-10-04 16:48:02" "2018-10-04 16:49:04" "2018-10-04 17:19:02" ...
## ..$ spots : int [1:6] 14424997 10504271 11014057 10741612 11405261 11263123
## ..$ bases : int [1:6] 735674847 535717821 553039487 547822212 570892854 574419273
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 51 51 50 51 50 51
## ..$ size_MB : int [1:6] 453 348 363 356 372 374
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965778/SRR7965778.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965780/SRR7965780.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965781/SRR7965781.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965787/SRR7965787.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP163478" "SRP163478" "SRP163478" "SRP163478" ...
## ..$ BioProject : chr [1:6] "PRJNA494710" "PRJNA494710" "PRJNA494710" "PRJNA494710" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 494710 494710 494710 494710 494710 494710
## ..$ Sample : chr [1:6] "SRS3878457" "SRS3878459" "SRS3878460" "SRS3878466" ...
## ..$ BioSample : chr [1:6] "SAMN10177851" "SAMN10177849" "SAMN10177848" "SAMN10177842" ...
## ..$ 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] "SRA789237" "SRA789237" "SRA789237" "SRA789237" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "9E0B2268CCC6C95DF8E198A1076580A4" "9417247CAD56F92EF193C78C5805FBAF" "647CDFE60C62CD0FBCAAB41692FA6A10" "C96C36EAFD8CAF570C72563E73D88111" ...
## ..$ ReadHash : chr [1:6] "47ADE033063C2F051258F35C37A7C1CF" "61FCB1E1F0B08AB39061852823B03AF0" "CA52A8E53EC33847D34244BE4338B337" "8D439EF6CE47F6D7B33FEA4326E537BE" ...
## $ 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
## SRP163478:right ventricle of left ventricular heart failure (LV-HF) versus right ventricle of biventricular heart failure (BiV-HF): LV-HF; SRX4799404, SRX4799405, SRX4799406, SRX4799407, SRX4799408: BiV-HF; SRX4799409, SRX4799410, SRX4799411, SRX4799412, SRX4799413;## 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:
## ..$ SRR7965781: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965783: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965784: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965787: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965788: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965789: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR7965781: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965783: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965784: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965787: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965788: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965789: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 6 variables:
## ..$ SRR7965781: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965783: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965784: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965787: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965788: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965789: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(5,7)" "WARN(5,7)" "FAIL(1,2,3,4,5,6,7)" "WARN(5,7)" ...
## ..$ SRX_accession: chr [1:6] "SRX4799404" "SRX4799406" "SRX4799407" "SRX4799410" ...
## ..$ SRS_accession: chr [1:6] "SRS3878460" "SRS3878462" "SRS3878463" "SRS3878466" ...
## ..$ SRP_accession: chr [1:6] "SRP163478" "SRP163478" "SRP163478" "SRP163478" ...
## ..$ Sample_name : chr [1:6] "GSM3417071" "GSM3417073" "GSM3417074" "GSM3417077" ...
## ..$ GEO_series : chr [1:6] "GSE120852" "GSE120852" "GSE120852" "GSE120852" ...
## ..$ 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)" "WARN(5,7)" "FAIL(1,2,3,4,5,6,7)" "WARN(5,7)" ...
## ..$ SRX_accession : chr [1:6] "SRX4799404" "SRX4799406" "SRX4799407" "SRX4799410" ...
## ..$ SRS_accession : chr [1:6] "SRS3878460" "SRS3878462" "SRS3878463" "SRS3878466" ...
## ..$ SRP_accession : chr [1:6] "SRP163478" "SRP163478" "SRP163478" "SRP163478" ...
## ..$ Sample_name : chr [1:6] "GSM3417071" "GSM3417073" "GSM3417074" "GSM3417077" ...
## ..$ GEO_series : chr [1:6] "GSE120852" "GSE120852" "GSE120852" "GSE120852" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM3417071" "GSM3417073" "GSM3417074" "GSM3417077" ...
## ..$ ReleaseDate : chr [1:6] "2018-10-08 18:32:08" "2018-10-08 18:32:08" "2018-10-08 18:32:08" "2018-10-08 18:32:08" ...
## ..$ LoadDate : chr [1:6] "2018-10-04 16:49:04" "2018-10-04 16:48:19" "2018-10-04 16:49:37" "2018-10-04 17:19:02" ...
## ..$ spots : int [1:6] 11014057 11472954 17053061 10741612 11405261 11263123
## ..$ bases : int [1:6] 553039487 585120654 869706111 547822212 570892854 574419273
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 50 51 51 51 50 51
## ..$ size_MB : int [1:6] 363 380 568 356 372 374
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965781/SRR7965781.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965783/SRR7965783.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965784/SRR7965784.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965787/SRR7965787.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP163478" "SRP163478" "SRP163478" "SRP163478" ...
## ..$ BioProject : chr [1:6] "PRJNA494710" "PRJNA494710" "PRJNA494710" "PRJNA494710" ...
## ..$ Study_Pubmed_id : int [1:6] 3 3 3 3 3 3
## ..$ ProjectID : int [1:6] 494710 494710 494710 494710 494710 494710
## ..$ Sample : chr [1:6] "SRS3878460" "SRS3878462" "SRS3878463" "SRS3878466" ...
## ..$ BioSample : chr [1:6] "SAMN10177848" "SAMN10177846" "SAMN10177845" "SAMN10177842" ...
## ..$ 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] "SRA789237" "SRA789237" "SRA789237" "SRA789237" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "647CDFE60C62CD0FBCAAB41692FA6A10" "A8F8B74766DE0B201954BA8A26F8ED29" "A4E34D007760E5AE10456AD48925AF68" "C96C36EAFD8CAF570C72563E73D88111" ...
## ..$ ReadHash : chr [1:6] "CA52A8E53EC33847D34244BE4338B337" "5639EED667595A511C577B330CF70AB8" "F6A3EB2478886BAD3B7C9ED3FE5FDE57" "8D439EF6CE47F6D7B33FEA4326E537BE" ...
## $ 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
## SRP163478: left ventricle of non-failing control versus left ventricle of left ventricular heart failure (LV-HF): control; SRX4799414, SRX4799415, SRX4799416, SRX4799417, SRX4799418: LV-HF; SRX4799419, SRX4799420, SRX4799421, SRX4799422, SRX4799423;## 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 1 variable:
## ..$ SRR7965796: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 1 variable:
## ..$ SRR7965796: 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 1 variable:
## ..$ SRR7965796: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 1 obs. of 7 variables:
## ..$ QC_summary : chr "WARN(5,7)"
## ..$ SRX_accession: chr "SRX4799419"
## ..$ SRS_accession: chr "SRS3878475"
## ..$ SRP_accession: chr "SRP163478"
## ..$ Sample_name : chr "GSM3417086"
## ..$ GEO_series : chr "GSE120852"
## ..$ Library_name : logi NA
## $ MetadataFull :'data.frame': 1 obs. of 52 variables:
## ..$ QC_summary : chr "WARN(5,7)"
## ..$ SRX_accession : chr "SRX4799419"
## ..$ SRS_accession : chr "SRS3878475"
## ..$ SRP_accession : chr "SRP163478"
## ..$ Sample_name : chr "GSM3417086"
## ..$ GEO_series : chr "GSE120852"
## ..$ Library_name : logi NA
## ..$ SampleName : chr "GSM3417086"
## ..$ ReleaseDate : chr "2018-10-08 18:32:08"
## ..$ LoadDate : chr "2018-10-04 16:48:38"
## ..$ spots : int 10994143
## ..$ bases : int 542735728
## ..$ spots_with_mates : int 0
## ..$ avgLength : int 49
## ..$ size_MB : int 335
## ..$ AssemblyName : logi NA
## ..$ download_path : chr "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965796/SRR7965796.1"
## ..$ LibraryName : logi NA
## ..$ LibraryStrategy : chr "RNA-Seq"
## ..$ LibrarySelection : chr "cDNA"
## ..$ LibrarySource : chr "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr "SINGLE"
## ..$ InsertSize : int 0
## ..$ InsertDev : num 0
## ..$ Platform : chr "ILLUMINA"
## ..$ Model : chr "Illumina HiSeq 2500"
## ..$ SRAStudy : chr "SRP163478"
## ..$ BioProject : chr "PRJNA494710"
## ..$ Study_Pubmed_id : int 3
## ..$ ProjectID : int 494710
## ..$ Sample : chr "SRS3878475"
## ..$ BioSample : chr "SAMN10177833"
## ..$ SampleType : chr "simple"
## ..$ TaxID : int 9606
## ..$ ScientificName : chr "Homo sapiens"
## ..$ g1k_pop_code : logi NA
## ..$ source : logi NA
## ..$ g1k_analysis_group : logi NA
## ..$ Subject_ID : logi NA
## ..$ Sex : logi NA
## ..$ Disease : logi NA
## ..$ Tumor : chr "no"
## ..$ Affection_Status : logi NA
## ..$ Analyte_Type : logi NA
## ..$ Histological_Type : logi NA
## ..$ Body_Site : logi NA
## ..$ CenterName : chr "GEO"
## ..$ Submission : chr "SRA789237"
## ..$ dbgap_study_accession: logi NA
## ..$ Consent : chr "public"
## ..$ RunHash : chr "B7CC9F57132CD2DC1DBB2866917D6350"
## ..$ ReadHash : chr "4B3DB0BEA95CEFBA812FA13467C17282"
## $ absent : chr(0)## SRP163478: left ventricle of non-failing control versus left ventricle of biventricular heart failure (BiV-HF): control; SRX4799414, SRX4799415, SRX4799416, SRX4799417, SRX4799418: BiV-HF; SRX4799424, SRX4799425, SRX4799426, SRX4799427, SRX4799428;
## 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:
## ..$ SRR7965801: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965802: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965804: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 3 variables:
## ..$ SRR7965801: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965802: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965804: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 3 variables:
## ..$ SRR7965801: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965802: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965804: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 3 obs. of 7 variables:
## ..$ QC_summary : chr [1:3] "PASS" "WARN(5)" "FAIL(1,2,3,4,5,6,7)"
## ..$ SRX_accession: chr [1:3] "SRX4799424" "SRX4799425" "SRX4799427"
## ..$ SRS_accession: chr [1:3] "SRS3878480" "SRS3878481" "SRS3878482"
## ..$ SRP_accession: chr [1:3] "SRP163478" "SRP163478" "SRP163478"
## ..$ Sample_name : chr [1:3] "GSM3417091" "GSM3417092" "GSM3417094"
## ..$ GEO_series : chr [1:3] "GSE120852" "GSE120852" "GSE120852"
## ..$ Library_name : logi [1:3] NA NA NA
## $ MetadataFull :'data.frame': 3 obs. of 52 variables:
## ..$ QC_summary : chr [1:3] "PASS" "WARN(5)" "FAIL(1,2,3,4,5,6,7)"
## ..$ SRX_accession : chr [1:3] "SRX4799424" "SRX4799425" "SRX4799427"
## ..$ SRS_accession : chr [1:3] "SRS3878480" "SRS3878481" "SRS3878482"
## ..$ SRP_accession : chr [1:3] "SRP163478" "SRP163478" "SRP163478"
## ..$ Sample_name : chr [1:3] "GSM3417091" "GSM3417092" "GSM3417094"
## ..$ GEO_series : chr [1:3] "GSE120852" "GSE120852" "GSE120852"
## ..$ Library_name : logi [1:3] NA NA NA
## ..$ SampleName : chr [1:3] "GSM3417091" "GSM3417092" "GSM3417094"
## ..$ ReleaseDate : chr [1:3] "2018-10-08 18:32:08" "2018-10-08 18:32:08" "2018-10-08 18:32:08"
## ..$ LoadDate : chr [1:3] "2018-10-04 16:48:38" "2018-10-04 16:48:49" "2018-10-04 16:48:42"
## ..$ spots : int [1:3] 14585869 14032054 14982702
## ..$ bases : int [1:3] 743879319 715634754 764117802
## ..$ spots_with_mates : int [1:3] 0 0 0
## ..$ avgLength : int [1:3] 51 51 51
## ..$ size_MB : int [1:3] 457 443 474
## ..$ AssemblyName : logi [1:3] NA NA NA
## ..$ download_path : chr [1:3] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965801/SRR7965801.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965802/SRR7965802.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965804/SRR7965804.1"
## ..$ LibraryName : logi [1:3] NA NA NA
## ..$ LibraryStrategy : chr [1:3] "RNA-Seq" "RNA-Seq" "RNA-Seq"
## ..$ LibrarySelection : chr [1:3] "cDNA" "cDNA" "cDNA"
## ..$ LibrarySource : chr [1:3] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr [1:3] "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] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500"
## ..$ SRAStudy : chr [1:3] "SRP163478" "SRP163478" "SRP163478"
## ..$ BioProject : chr [1:3] "PRJNA494710" "PRJNA494710" "PRJNA494710"
## ..$ Study_Pubmed_id : int [1:3] 3 3 3
## ..$ ProjectID : int [1:3] 494710 494710 494710
## ..$ Sample : chr [1:3] "SRS3878480" "SRS3878481" "SRS3878482"
## ..$ BioSample : chr [1:3] "SAMN10177828" "SAMN10177827" "SAMN10177825"
## ..$ 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] "SRA789237" "SRA789237" "SRA789237"
## ..$ dbgap_study_accession: logi [1:3] NA NA NA
## ..$ Consent : chr [1:3] "public" "public" "public"
## ..$ RunHash : chr [1:3] "48B1A6806BF44C96E6DBB9D0B416CB89" "6DEB9D521CA94471BE490981D988660B" "32F6EB5F940702C0BD6651E914247066"
## ..$ ReadHash : chr [1:3] "8EAF3D3BE1D8DEAB17EA07622716D4C9" "950FA4CF9F7ACD171E3682DD04C8325A" "BA6F503E4E70414D07D7068F76728B23"
## $ absent : chr(0)## SRP163478: left ventricle of left ventricular heart failure (LV-HF) versus left ventricle of biventricular heart failure (BiV-HF): LV-HF; SRX4799419, SRX4799420, SRX4799421, SRX4799422, SRX4799423: BiV-HF; SRX4799424, SRX4799425, SRX4799426, SRX4799427, SRX4799428;
## 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:
## ..$ SRR7965800: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965801: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965802: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965804: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 4 variables:
## ..$ SRR7965800: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965801: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965802: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7965804: int [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 4 variables:
## ..$ SRR7965800: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965801: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965802: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR7965804: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 4 obs. of 7 variables:
## ..$ QC_summary : chr [1:4] "PASS" "PASS" "WARN(5)" "FAIL(1,2,3,4,5,6,7)"
## ..$ SRX_accession: chr [1:4] "SRX4799423" "SRX4799424" "SRX4799425" "SRX4799427"
## ..$ SRS_accession: chr [1:4] "SRS3878479" "SRS3878480" "SRS3878481" "SRS3878482"
## ..$ SRP_accession: chr [1:4] "SRP163478" "SRP163478" "SRP163478" "SRP163478"
## ..$ Sample_name : chr [1:4] "GSM3417090" "GSM3417091" "GSM3417092" "GSM3417094"
## ..$ GEO_series : chr [1:4] "GSE120852" "GSE120852" "GSE120852" "GSE120852"
## ..$ 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(5)" "FAIL(1,2,3,4,5,6,7)"
## ..$ SRX_accession : chr [1:4] "SRX4799423" "SRX4799424" "SRX4799425" "SRX4799427"
## ..$ SRS_accession : chr [1:4] "SRS3878479" "SRS3878480" "SRS3878481" "SRS3878482"
## ..$ SRP_accession : chr [1:4] "SRP163478" "SRP163478" "SRP163478" "SRP163478"
## ..$ Sample_name : chr [1:4] "GSM3417090" "GSM3417091" "GSM3417092" "GSM3417094"
## ..$ GEO_series : chr [1:4] "GSE120852" "GSE120852" "GSE120852" "GSE120852"
## ..$ Library_name : logi [1:4] NA NA NA NA
## ..$ SampleName : chr [1:4] "GSM3417090" "GSM3417091" "GSM3417092" "GSM3417094"
## ..$ ReleaseDate : chr [1:4] "2018-10-08 18:32:08" "2018-10-08 18:32:08" "2018-10-08 18:32:08" "2018-10-08 18:32:08"
## ..$ LoadDate : chr [1:4] "2018-10-04 16:48:50" "2018-10-04 16:48:38" "2018-10-04 16:48:49" "2018-10-04 16:48:42"
## ..$ spots : int [1:4] 14878631 14585869 14032054 14982702
## ..$ bases : int [1:4] 758810181 743879319 715634754 764117802
## ..$ spots_with_mates : int [1:4] 0 0 0 0
## ..$ avgLength : int [1:4] 51 51 51 51
## ..$ size_MB : int [1:4] 468 457 443 474
## ..$ AssemblyName : logi [1:4] NA NA NA NA
## ..$ download_path : chr [1:4] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965800/SRR7965800.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965801/SRR7965801.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965802/SRR7965802.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7965804/SRR7965804.1"
## ..$ LibraryName : logi [1:4] NA NA NA NA
## ..$ LibraryStrategy : chr [1:4] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq"
## ..$ LibrarySelection : chr [1:4] "cDNA" "cDNA" "cDNA" "cDNA"
## ..$ LibrarySource : chr [1:4] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr [1:4] "SINGLE" "SINGLE" "SINGLE" "SINGLE"
## ..$ InsertSize : int [1:4] 0 0 0 0
## ..$ InsertDev : num [1:4] 0 0 0 0
## ..$ Platform : chr [1:4] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA"
## ..$ Model : chr [1:4] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500"
## ..$ SRAStudy : chr [1:4] "SRP163478" "SRP163478" "SRP163478" "SRP163478"
## ..$ BioProject : chr [1:4] "PRJNA494710" "PRJNA494710" "PRJNA494710" "PRJNA494710"
## ..$ Study_Pubmed_id : int [1:4] 3 3 3 3
## ..$ ProjectID : int [1:4] 494710 494710 494710 494710
## ..$ Sample : chr [1:4] "SRS3878479" "SRS3878480" "SRS3878481" "SRS3878482"
## ..$ BioSample : chr [1:4] "SAMN10177829" "SAMN10177828" "SAMN10177827" "SAMN10177825"
## ..$ 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] "SRA789237" "SRA789237" "SRA789237" "SRA789237"
## ..$ dbgap_study_accession: logi [1:4] NA NA NA NA
## ..$ Consent : chr [1:4] "public" "public" "public" "public"
## ..$ RunHash : chr [1:4] "0398799E9A6A4EA2F904E28699F4BEC1" "48B1A6806BF44C96E6DBB9D0B416CB89" "6DEB9D521CA94471BE490981D988660B" "32F6EB5F940702C0BD6651E914247066"
## ..$ ReadHash : chr [1:4] "CE389E66FB968E34E5B7FA73ECFB4CE5" "8EAF3D3BE1D8DEAB17EA07622716D4C9" "950FA4CF9F7ACD171E3682DD04C8325A" "BA6F503E4E70414D07D7068F76728B23"
## $ absent : chr(0)## SRP162743: patients with a non-inflammatory dilated cardiomyopathy (DCM) versus patients with acute myocarditis:DCM; SRX4744907, SRX4744908, SRX4744909, SRX4744910,SRX4744911, SRX4744912, SRX4744913, SRX4744914, SRX4744915, SRX4744916, SRX4744917: myocarditis; SRX4744918, SRX4744919, SRX4744920, SRX4744921, SRX4744922; age
## 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:
## ..$ SRR7908791: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR7908792: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR7908793: int [1:58302] 0 7 1 0 0 0 0 0 0 0 ...
## ..$ SRR7908795: int [1:58302] 0 6 1 0 0 0 0 0 0 0 ...
## ..$ SRR7908796: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR7908791: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7908792: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7908793: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7908795: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR7908796: 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:
## ..$ SRR7908791: chr [1:30] "PE" "Sanger/Illumina1.9" "75" "75" ...
## ..$ SRR7908792: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR7908793: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR7908795: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR7908796: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "WARN(6,8)" "FAIL(2)" "WARN(8)" "FAIL(2)" ...
## ..$ SRX_accession: chr [1:5] "SRX4744917" "SRX4744918" "SRX4744919" "SRX4744921" ...
## ..$ SRS_accession: chr [1:5] "SRS3825591" "SRS3825587" "SRS3825590" "SRS3825589" ...
## ..$ SRP_accession: chr [1:5] "SRP162743" "SRP162743" "SRP162743" "SRP162743" ...
## ..$ Sample_name : chr [1:5] "GSM3403244" "GSM3403245" "GSM3403246" "GSM3403248" ...
## ..$ GEO_series : chr [1:5] "GSE120567" "GSE120567" "GSE120567" "GSE120567" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "WARN(6,8)" "FAIL(2)" "WARN(8)" "FAIL(2)" ...
## ..$ SRX_accession : chr [1:5] "SRX4744917" "SRX4744918" "SRX4744919" "SRX4744921" ...
## ..$ SRS_accession : chr [1:5] "SRS3825591" "SRS3825587" "SRS3825590" "SRS3825589" ...
## ..$ SRP_accession : chr [1:5] "SRP162743" "SRP162743" "SRP162743" "SRP162743" ...
## ..$ Sample_name : chr [1:5] "GSM3403244" "GSM3403245" "GSM3403246" "GSM3403248" ...
## ..$ GEO_series : chr [1:5] "GSE120567" "GSE120567" "GSE120567" "GSE120567" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM3403244" "GSM3403245" "GSM3403246" "GSM3403248" ...
## ..$ ReleaseDate : chr [1:5] "2018-10-01 10:26:20" "2018-10-01 10:26:20" "2018-10-01 10:26:20" "2018-10-01 10:26:20" ...
## ..$ LoadDate : chr [1:5] "2018-09-27 11:51:00" "2018-09-27 11:55:50" "2018-09-27 11:49:27" "2018-09-27 11:50:45" ...
## ..$ spots : int [1:5] 54847340 43212732 33597025 35593913 41376726
## ..$ bases : num [1:5] 8.23e+09 8.64e+09 6.72e+09 7.12e+09 8.28e+09
## ..$ spots_with_mates : int [1:5] 54847340 43212732 33597025 35593913 41376726
## ..$ avgLength : int [1:5] 150 200 200 200 200
## ..$ size_MB : int [1:5] 5037 5280 3905 4151 4868
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7908791/SRR7908791.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7908792/SRR7908792.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7908793/SRR7908793.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-2/SRR7908795/SRR7908795.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:5] "SRP162743" "SRP162743" "SRP162743" "SRP162743" ...
## ..$ BioProject : chr [1:5] "PRJNA493608" "PRJNA493608" "PRJNA493608" "PRJNA493608" ...
## ..$ Study_Pubmed_id : int [1:5] 3 3 3 3 3
## ..$ ProjectID : int [1:5] 493608 493608 493608 493608 493608
## ..$ Sample : chr [1:5] "SRS3825591" "SRS3825587" "SRS3825590" "SRS3825589" ...
## ..$ BioSample : chr [1:5] "SAMN10137821" "SAMN10137820" "SAMN10137819" "SAMN10137817" ...
## ..$ 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] "SRA784836" "SRA784836" "SRA784836" "SRA784836" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "14ECFFDBD03FA88733F3D9F31CFD3D0D" "0F6C45C6D37CB55A241120A1A83F53A0" "00055C8015F45FC38A13CACDACE9F8DA" "29A6A7EF653D5BECA3CF048A2E1789D9" ...
## ..$ ReadHash : chr [1:5] "0F161E89E9865F50C5206DCF374C14A2" "BF881AA92C3FD5E9726F7F8C93F256B2" "81D09AAE2212A45CFE0D351076DA98FC" "7E446CC50844D4C9FDBDD7E9F37A3C50" ...
## $ absent : chr(0)## SRP018779: non-silencing control versus TCF21 knockdown:non-silencing control; SRX243750, SRX243751, SRX243752: TCF21; SRX243753, SRX243754, SRX243755;
## 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:
## ..$ SRR748305: int [1:58302] 0 10 0 0 0 0 0 0 0 2 ...
## ..$ SRR748306: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR748307: int [1:58302] 0 9 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 3 variables:
## ..$ SRR748305: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR748306: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR748307: 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:
## ..$ SRR748305: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR748306: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR748307: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 3 obs. of 7 variables:
## ..$ QC_summary : chr [1:3] "FAIL(2)" "FAIL(2)" "FAIL(2)"
## ..$ SRX_accession: chr [1:3] "SRX243753" "SRX243754" "SRX243755"
## ..$ SRS_accession: chr [1:3] "SRS397044" "SRS397045" "SRS397046"
## ..$ SRP_accession: chr [1:3] "SRP018779" "SRP018779" "SRP018779"
## ..$ Sample_name : chr [1:3] "GSM1085739" "GSM1085740" "GSM1085741"
## ..$ GEO_series : chr [1:3] "GSE44461" "GSE44461" "GSE44461"
## ..$ Library_name : logi [1:3] NA NA NA
## $ MetadataFull :'data.frame': 3 obs. of 52 variables:
## ..$ QC_summary : chr [1:3] "FAIL(2)" "FAIL(2)" "FAIL(2)"
## ..$ SRX_accession : chr [1:3] "SRX243753" "SRX243754" "SRX243755"
## ..$ SRS_accession : chr [1:3] "SRS397044" "SRS397045" "SRS397046"
## ..$ SRP_accession : chr [1:3] "SRP018779" "SRP018779" "SRP018779"
## ..$ Sample_name : chr [1:3] "GSM1085739" "GSM1085740" "GSM1085741"
## ..$ GEO_series : chr [1:3] "GSE44461" "GSE44461" "GSE44461"
## ..$ Library_name : logi [1:3] NA NA NA
## ..$ SampleName : chr [1:3] "GSM1085739" "GSM1085740" "GSM1085741"
## ..$ ReleaseDate : chr [1:3] "2015-03-19 15:52:21" "2015-03-19 15:52:21" "2015-03-19 15:52:21"
## ..$ LoadDate : chr [1:3] "2013-02-22 03:34:03" "2013-02-22 03:36:33" "2013-02-22 03:40:51"
## ..$ spots : int [1:3] 35311375 32550924 37508331
## ..$ bases : num [1:3] 7.06e+09 6.51e+09 7.50e+09
## ..$ spots_with_mates : int [1:3] 35311375 32550924 37508331
## ..$ avgLength : int [1:3] 200 200 200
## ..$ size_MB : int [1:3] 4640 4282 4941
## ..$ AssemblyName : logi [1:3] NA NA NA
## ..$ download_path : chr [1:3] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR748305/SRR748305.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR748306/SRR748306.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR748307/SRR748307.1"
## ..$ LibraryName : logi [1:3] NA NA NA
## ..$ LibraryStrategy : chr [1:3] "RNA-Seq" "RNA-Seq" "RNA-Seq"
## ..$ LibrarySelection : chr [1:3] "cDNA" "cDNA" "cDNA"
## ..$ LibrarySource : chr [1:3] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC"
## ..$ LibraryLayout : chr [1:3] "PAIRED" "PAIRED" "PAIRED"
## ..$ InsertSize : int [1:3] 0 0 0
## ..$ InsertDev : num [1:3] 0 0 0
## ..$ Platform : chr [1:3] "ILLUMINA" "ILLUMINA" "ILLUMINA"
## ..$ Model : chr [1:3] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000"
## ..$ SRAStudy : chr [1:3] "SRP018779" "SRP018779" "SRP018779"
## ..$ BioProject : chr [1:3] "PRJNA191801" "PRJNA191801" "PRJNA191801"
## ..$ Study_Pubmed_id : int [1:3] 2 2 2
## ..$ ProjectID : int [1:3] 191801 191801 191801
## ..$ Sample : chr [1:3] "SRS397044" "SRS397045" "SRS397046"
## ..$ BioSample : chr [1:3] "SAMN01923912" "SAMN01923913" "SAMN01923914"
## ..$ 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] "SRA067483" "SRA067483" "SRA067483"
## ..$ dbgap_study_accession: logi [1:3] NA NA NA
## ..$ Consent : chr [1:3] "public" "public" "public"
## ..$ RunHash : chr [1:3] "90F6E523648583B528015E94A34AAE88" "3A50E334F5BAFD327E52CC79AC600256" "ACC84F627A4074DB56F469895AC915A6"
## ..$ ReadHash : chr [1:3] "F1A87C041484208D3B10DCB09AC7BC83" "FD4BD1F258E279636D9FB561E0FA043C" "891E6433ED529D9C6EECCEF9AF301DB2"
## $ absent : chr(0)## SRP126861: left ventricle samples in non-ischemic cardiomyopathy (NICM) versus ischemic cardiomyopathy (ISCH): NICM; SRX3474755, SRX3474756, SRX3474758, SRX3474760, SRX3474761, SRX3474762: ISCH; SRX3474757, SRX3474759, SRX3474763, SRX3474764, SRX3474765; sex, race
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 8 variables:
## ..$ SRR6380728: int [1:58302] 0 43 2 0 0 0 0 0 0 1 ...
## ..$ SRR6380729: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380731: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380733: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR6380734: int [1:58302] 0 12 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380736: int [1:58302] 0 6 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380737: int [1:58302] 0 25 1 0 0 0 0 0 0 0 ...
## ..$ SRR6380738: int [1:58302] 0 8 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 8 variables:
## ..$ SRR6380728: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380729: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380731: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380733: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380734: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380736: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380737: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR6380738: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 8 variables:
## ..$ SRR6380728: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6380729: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6380731: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6380733: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6380734: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6380736: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6380737: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR6380738: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "51" ...
## $ MetadataSummary:'data.frame': 8 obs. of 7 variables:
## ..$ QC_summary : chr [1:8] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:8] "SRX3474755" "SRX3474756" "SRX3474758" "SRX3474760" ...
## ..$ SRS_accession: chr [1:8] "SRS2761139" "SRS2761127" "SRS2761129" "SRS2761131" ...
## ..$ SRP_accession: chr [1:8] "SRP126861" "SRP126861" "SRP126861" "SRP126861" ...
## ..$ Sample_name : chr [1:8] "GSM2891378" "GSM2891379" "GSM2891381" "GSM2891383" ...
## ..$ GEO_series : chr [1:8] "GSE108157" "GSE108157" "GSE108157" "GSE108157" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 8 obs. of 52 variables:
## ..$ QC_summary : chr [1:8] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:8] "SRX3474755" "SRX3474756" "SRX3474758" "SRX3474760" ...
## ..$ SRS_accession : chr [1:8] "SRS2761139" "SRS2761127" "SRS2761129" "SRS2761131" ...
## ..$ SRP_accession : chr [1:8] "SRP126861" "SRP126861" "SRP126861" "SRP126861" ...
## ..$ Sample_name : chr [1:8] "GSM2891378" "GSM2891379" "GSM2891381" "GSM2891383" ...
## ..$ GEO_series : chr [1:8] "GSE108157" "GSE108157" "GSE108157" "GSE108157" ...
## ..$ Library_name : logi [1:8] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:8] "GSM2891378" "GSM2891379" "GSM2891381" "GSM2891383" ...
## ..$ ReleaseDate : chr [1:8] "2018-08-22 19:15:06" "2018-08-22 19:15:06" "2018-08-22 19:15:06" "2018-08-22 19:15:06" ...
## ..$ LoadDate : chr [1:8] "2017-12-15 16:06:29" "2017-12-15 16:07:05" "2017-12-15 16:05:21" "2017-12-15 16:05:34" ...
## ..$ spots : int [1:8] 35201776 37278697 36038191 34024931 40214246 40837514 54522774 31745515
## ..$ bases : num [1:8] 3.59e+09 3.80e+09 3.68e+09 3.47e+09 4.10e+09 ...
## ..$ spots_with_mates : int [1:8] 35201776 37278697 36038191 34024931 40214246 40837514 54522774 31745515
## ..$ avgLength : int [1:8] 102 102 102 102 102 102 102 102
## ..$ size_MB : int [1:8] 1550 1636 1586 1499 1776 1782 2426 1406
## ..$ AssemblyName : logi [1:8] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:8] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6380728/SRR6380728.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6380729/SRR6380729.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6380731/SRR6380731.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-11/SRR6380733/SRR6380733.1" ...
## ..$ LibraryName : logi [1:8] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:8] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:8] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:8] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:8] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:8] 0 0 0 0 0 0 0 0
## ..$ InsertDev : num [1:8] 0 0 0 0 0 0 0 0
## ..$ Platform : chr [1:8] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:8] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:8] "SRP126861" "SRP126861" "SRP126861" "SRP126861" ...
## ..$ BioProject : chr [1:8] "PRJNA422603" "PRJNA422603" "PRJNA422603" "PRJNA422603" ...
## ..$ Study_Pubmed_id : int [1:8] 3 3 3 3 3 3 3 3
## ..$ ProjectID : int [1:8] 422603 422603 422603 422603 422603 422603 422603 422603
## ..$ Sample : chr [1:8] "SRS2761139" "SRS2761127" "SRS2761129" "SRS2761131" ...
## ..$ BioSample : chr [1:8] "SAMN08182866" "SAMN08182865" "SAMN08182863" "SAMN08182861" ...
## ..$ SampleType : chr [1:8] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:8] 9606 9606 9606 9606 9606 9606 9606 9606
## ..$ ScientificName : chr [1:8] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:8] NA NA NA NA NA NA ...
## ..$ source : logi [1:8] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:8] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:8] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:8] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:8] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:8] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:8] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:8] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:8] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:8] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:8] "SRA639261" "SRA639261" "SRA639261" "SRA639261" ...
## ..$ dbgap_study_accession: logi [1:8] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:8] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:8] "86578320E90E94EED6C4416701DD8CE9" "BFE586BA1E68FD7889B51CFA23F94BD5" "90F75FFE5B946835AADDAA4ED1E5F68C" "1D761984981F8886C624CAB669DBA12F" ...
## ..$ ReadHash : chr [1:8] "B59941C4894B0BE26703A6F8491FB201" "2BF34FCC26A190515F9FDF822798583E" "0927FC2D5360B7753E5263AD54E53DDF" "CE12CA9EB8AC9C6236CFAB80D639497E" ...
## $ 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
## SRP108065: control versus left ventricle of pediatric idiopathic dilated cardiomyopathy patients: control; SRX2858506, SRX2858508, SRX2858509, SRX2858511, SRX2858512, SRX2858513, SRX2858517: idopathic dilated cardiomyopathy; SRX2858505, SRX2858507, SRX2858510, SRX2858514, SRX2858515, SRX2858516, SRX2858518;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 14 variables:
## ..$ SRR5605970: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605971: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605972: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605973: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605974: int [1:58302] 0 7 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605975: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605976: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605977: int [1:58302] 0 2 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605978: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605979: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605980: int [1:58302] 0 1 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605981: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605982: int [1:58302] 0 2 0 0 0 0 0 0 0 1 ...
## ..$ SRR5605983: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 14 variables:
## ..$ SRR5605970: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605971: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605972: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605973: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605974: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605975: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605976: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605977: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605978: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605979: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605980: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605981: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605982: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5605983: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 14 variables:
## ..$ SRR5605970: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5605971: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5605972: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5605973: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5605974: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5605975: chr [1:30] "SE" "Sanger/Illumina1.9" "51" "51" ...
## ..$ SRR5605976: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5605977: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5605978: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5605979: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5605980: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5605981: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5605982: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## ..$ SRR5605983: chr [1:30] "SE" "Sanger/Illumina1.9" "50" "50" ...
## $ MetadataSummary:'data.frame': 14 obs. of 7 variables:
## ..$ QC_summary : chr [1:14] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:14] "SRX2858505" "SRX2858506" "SRX2858507" "SRX2858508" ...
## ..$ SRS_accession: chr [1:14] "SRS2229192" "SRS2229193" "SRS2229194" "SRS2229195" ...
## ..$ SRP_accession: chr [1:14] "SRP108065" "SRP108065" "SRP108065" "SRP108065" ...
## ..$ Sample_name : chr [1:14] "GSM2641079" "GSM2641080" "GSM2641081" "GSM2641082" ...
## ..$ GEO_series : chr [1:14] "GSE99321" "GSE99321" "GSE99321" "GSE99321" ...
## ..$ Library_name : logi [1:14] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 14 obs. of 52 variables:
## ..$ QC_summary : chr [1:14] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:14] "SRX2858505" "SRX2858506" "SRX2858507" "SRX2858508" ...
## ..$ SRS_accession : chr [1:14] "SRS2229192" "SRS2229193" "SRS2229194" "SRS2229195" ...
## ..$ SRP_accession : chr [1:14] "SRP108065" "SRP108065" "SRP108065" "SRP108065" ...
## ..$ Sample_name : chr [1:14] "GSM2641079" "GSM2641080" "GSM2641081" "GSM2641082" ...
## ..$ GEO_series : chr [1:14] "GSE99321" "GSE99321" "GSE99321" "GSE99321" ...
## ..$ Library_name : logi [1:14] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:14] "GSM2641079" "GSM2641080" "GSM2641081" "GSM2641082" ...
## ..$ ReleaseDate : chr [1:14] "2017-09-06 16:06:12" "2017-09-06 16:06:12" "2017-09-06 16:06:12" "2017-09-06 16:06:12" ...
## ..$ LoadDate : chr [1:14] "2017-05-25 15:39:26" "2017-05-25 15:39:46" "2017-05-25 15:41:27" "2017-05-25 15:40:17" ...
## ..$ spots : int [1:14] 38837917 40903452 41200590 39708247 39078067 39452750 51776617 33633454 24286077 48495992 ...
## ..$ bases : num [1:14] 1.98e+09 2.09e+09 2.10e+09 2.03e+09 1.99e+09 ...
## ..$ spots_with_mates : int [1:14] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:14] 51 51 51 51 51 51 50 50 50 50 ...
## ..$ size_MB : int [1:14] 796 828 844 816 805 812 1651 1081 781 1542 ...
## ..$ AssemblyName : logi [1:14] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:14] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5605970/SRR5605970.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5605971/SRR5605971.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5605972/SRR5605972.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5605973/SRR5605973.1" ...
## ..$ LibraryName : logi [1:14] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:14] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:14] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:14] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:14] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:14] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:14] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:14] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:14] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:14] "SRP108065" "SRP108065" "SRP108065" "SRP108065" ...
## ..$ BioProject : chr [1:14] "PRJNA388098" "PRJNA388098" "PRJNA388098" "PRJNA388098" ...
## ..$ Study_Pubmed_id : int [1:14] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:14] 388098 388098 388098 388098 388098 388098 388098 388098 388098 388098 ...
## ..$ Sample : chr [1:14] "SRS2229192" "SRS2229193" "SRS2229194" "SRS2229195" ...
## ..$ BioSample : chr [1:14] "SAMN07169094" "SAMN07169107" "SAMN07169106" "SAMN07169105" ...
## ..$ SampleType : chr [1:14] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:14] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:14] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:14] NA NA NA NA NA NA ...
## ..$ source : logi [1:14] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:14] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:14] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:14] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:14] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:14] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:14] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:14] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:14] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:14] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:14] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:14] "SRA566756" "SRA566756" "SRA566756" "SRA566756" ...
## ..$ dbgap_study_accession: logi [1:14] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:14] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:14] "FCF13D121616187428A34CBAEEFE0B1D" "35262A483DCADBFCBCD18BBBA60C9F87" "BB6ABB8A0EC961E39845A986B8FDE419" "C37EC05533D86DD1888D9455D3D42BD2" ...
## ..$ ReadHash : chr [1:14] "EEF880B3EF2243B5A130FDF1C3B66199" "BC64647FD0BEEC703BD539D9E397F5D4" "9809C4A69C4CDDE829B13B4235C6F9CB" "2895B2EAAC94B7C85938640F3049D890" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 368 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP107288: control versus polyI-C treated cardiac progenitors: control; SRX2827481, SRX2827482, SRX2827483: polyI-C; SRX2827487, SRX2827488, SRX2827489;## 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:
## ..$ SRR5567131: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR5567132: int [1:58302] 0 2 3 0 0 0 0 0 0 0 ...
## ..$ SRR5567137: int [1:58302] 0 3 5 0 0 0 0 0 0 0 ...
## ..$ SRR5567138: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR5567139: int [1:58302] 0 3 4 1 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR5567131: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567132: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567137: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567138: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567139: 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:
## ..$ SRR5567131: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567132: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567137: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567138: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567139: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:5] "SRX2827481" "SRX2827482" "SRX2827487" "SRX2827488" ...
## ..$ SRS_accession: chr [1:5] "SRS2203349" "SRS2203350" "SRS2203355" "SRS2203356" ...
## ..$ SRP_accession: chr [1:5] "SRP107288" "SRP107288" "SRP107288" "SRP107288" ...
## ..$ Sample_name : chr [1:5] "GSM2628164" "GSM2628165" "GSM2628170" "GSM2628171" ...
## ..$ GEO_series : chr [1:5] "GSE98941" "GSE98941" "GSE98941" "GSE98941" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:5] "SRX2827481" "SRX2827482" "SRX2827487" "SRX2827488" ...
## ..$ SRS_accession : chr [1:5] "SRS2203349" "SRS2203350" "SRS2203355" "SRS2203356" ...
## ..$ SRP_accession : chr [1:5] "SRP107288" "SRP107288" "SRP107288" "SRP107288" ...
## ..$ Sample_name : chr [1:5] "GSM2628164" "GSM2628165" "GSM2628170" "GSM2628171" ...
## ..$ GEO_series : chr [1:5] "GSE98941" "GSE98941" "GSE98941" "GSE98941" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM2628164" "GSM2628165" "GSM2628170" "GSM2628171" ...
## ..$ ReleaseDate : chr [1:5] "2018-08-02 07:04:17" "2018-08-02 07:04:17" "2018-08-02 07:04:17" "2018-08-02 07:04:17" ...
## ..$ LoadDate : chr [1:5] "2017-05-15 23:45:10" "2017-05-15 23:43:30" "2017-05-15 23:45:05" "2017-05-15 23:43:44" ...
## ..$ spots : int [1:5] 17997709 19756134 22177141 21788812 23221113
## ..$ bases : num [1:5] 1.82e+09 2.00e+09 2.24e+09 2.20e+09 2.35e+09
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 101 101 101 101 101
## ..$ size_MB : int [1:5] 526 580 651 638 682
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567131/SRR5567131.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567132/SRR5567132.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567137/SRR5567137.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567138/SRR5567138.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:5] "SRP107288" "SRP107288" "SRP107288" "SRP107288" ...
## ..$ BioProject : chr [1:5] "PRJNA386871" "PRJNA386871" "PRJNA386871" "PRJNA386871" ...
## ..$ Study_Pubmed_id : logi [1:5] NA NA NA NA NA
## ..$ ProjectID : int [1:5] 386871 386871 386871 386871 386871
## ..$ Sample : chr [1:5] "SRS2203349" "SRS2203350" "SRS2203355" "SRS2203356" ...
## ..$ BioSample : chr [1:5] "SAMN07125618" "SAMN07125626" "SAMN07125621" "SAMN07125620" ...
## ..$ 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] "SRA561905" "SRA561905" "SRA561905" "SRA561905" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "EE7E7657BF1B3912D672B3943D5556F8" "A514F954CC0458E98E9E1974DDF03C54" "062573BAF6908A6FFC1DC9CC91FF7B42" "2DD7C2FC4F794A89CF74D200302F0086" ...
## ..$ ReadHash : chr [1:5] "834B261C3F1D4859F5AC5A0B7707501A" "4A698C48F1ED2FCD5A988737CC84547D" "2C80E038816A559A31CF92C18336FE67" "E9B9EC8AFEBD7986612D1DC001C690CC" ...
## $ 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
## SRP107288: control versus TGFbeta treated cardiac progenitors:control; SRX2827481, SRX2827482, SRX2827483: TGFbeta; SRX2827484, SRX2827485, SRX2827486;## 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:
## ..$ SRR5567131: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR5567132: int [1:58302] 0 2 3 0 0 0 0 0 0 0 ...
## ..$ SRR5567134: int [1:58302] 0 2 2 0 0 0 0 0 0 1 ...
## ..$ SRR5567135: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR5567136: int [1:58302] 0 0 3 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 5 variables:
## ..$ SRR5567131: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567132: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567134: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567135: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567136: 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:
## ..$ SRR5567131: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567132: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567134: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567135: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567136: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 5 obs. of 7 variables:
## ..$ QC_summary : chr [1:5] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:5] "SRX2827481" "SRX2827482" "SRX2827484" "SRX2827485" ...
## ..$ SRS_accession: chr [1:5] "SRS2203349" "SRS2203350" "SRS2203352" "SRS2203353" ...
## ..$ SRP_accession: chr [1:5] "SRP107288" "SRP107288" "SRP107288" "SRP107288" ...
## ..$ Sample_name : chr [1:5] "GSM2628164" "GSM2628165" "GSM2628167" "GSM2628168" ...
## ..$ GEO_series : chr [1:5] "GSE98941" "GSE98941" "GSE98941" "GSE98941" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## $ MetadataFull :'data.frame': 5 obs. of 52 variables:
## ..$ QC_summary : chr [1:5] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:5] "SRX2827481" "SRX2827482" "SRX2827484" "SRX2827485" ...
## ..$ SRS_accession : chr [1:5] "SRS2203349" "SRS2203350" "SRS2203352" "SRS2203353" ...
## ..$ SRP_accession : chr [1:5] "SRP107288" "SRP107288" "SRP107288" "SRP107288" ...
## ..$ Sample_name : chr [1:5] "GSM2628164" "GSM2628165" "GSM2628167" "GSM2628168" ...
## ..$ GEO_series : chr [1:5] "GSE98941" "GSE98941" "GSE98941" "GSE98941" ...
## ..$ Library_name : logi [1:5] NA NA NA NA NA
## ..$ SampleName : chr [1:5] "GSM2628164" "GSM2628165" "GSM2628167" "GSM2628168" ...
## ..$ ReleaseDate : chr [1:5] "2018-08-02 07:04:17" "2018-08-02 07:04:17" "2018-08-02 07:04:17" "2018-08-02 07:04:17" ...
## ..$ LoadDate : chr [1:5] "2017-05-15 23:45:10" "2017-05-15 23:43:30" "2017-05-15 23:44:25" "2017-05-15 23:45:23" ...
## ..$ spots : int [1:5] 17997709 19756134 21589850 23079514 20856857
## ..$ bases : num [1:5] 1.82e+09 2.00e+09 2.18e+09 2.33e+09 2.11e+09
## ..$ spots_with_mates : int [1:5] 0 0 0 0 0
## ..$ avgLength : int [1:5] 101 101 101 101 101
## ..$ size_MB : int [1:5] 526 580 634 675 610
## ..$ AssemblyName : logi [1:5] NA NA NA NA NA
## ..$ download_path : chr [1:5] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567131/SRR5567131.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567132/SRR5567132.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567134/SRR5567134.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567135/SRR5567135.1" ...
## ..$ LibraryName : logi [1:5] NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:5] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:5] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:5] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:5] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:5] 0 0 0 0 0
## ..$ InsertDev : num [1:5] 0 0 0 0 0
## ..$ Platform : chr [1:5] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:5] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:5] "SRP107288" "SRP107288" "SRP107288" "SRP107288" ...
## ..$ BioProject : chr [1:5] "PRJNA386871" "PRJNA386871" "PRJNA386871" "PRJNA386871" ...
## ..$ Study_Pubmed_id : logi [1:5] NA NA NA NA NA
## ..$ ProjectID : int [1:5] 386871 386871 386871 386871 386871
## ..$ Sample : chr [1:5] "SRS2203349" "SRS2203350" "SRS2203352" "SRS2203353" ...
## ..$ BioSample : chr [1:5] "SAMN07125618" "SAMN07125626" "SAMN07125624" "SAMN07125623" ...
## ..$ 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] "SRA561905" "SRA561905" "SRA561905" "SRA561905" ...
## ..$ dbgap_study_accession: logi [1:5] NA NA NA NA NA
## ..$ Consent : chr [1:5] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:5] "EE7E7657BF1B3912D672B3943D5556F8" "A514F954CC0458E98E9E1974DDF03C54" "D8E078F3727DF6E48031252F936DCB47" "AC134514FCC293816E2A1D9335D06DFD" ...
## ..$ ReadHash : chr [1:5] "834B261C3F1D4859F5AC5A0B7707501A" "4A698C48F1ED2FCD5A988737CC84547D" "7C791F4057FE6AF24AE3724D4E2F8756" "8367FE521AD98E2131DE30F3EA129659" ...
## $ 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
## SRP107288: polyI-C treated cardiac progenitors versus TGFbeta treated cardiac progenitors: polyI-C; SRX2827487, SRX2827488, SRX2827489: TGFbeta; SRX2827484, SRX2827485, SRX2827486;## 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:
## ..$ SRR5567134: int [1:58302] 0 2 2 0 0 0 0 0 0 1 ...
## ..$ SRR5567135: int [1:58302] 0 2 1 0 0 0 0 0 0 0 ...
## ..$ SRR5567136: int [1:58302] 0 0 3 0 0 0 0 0 0 0 ...
## ..$ SRR5567137: int [1:58302] 0 3 5 0 0 0 0 0 0 0 ...
## ..$ SRR5567138: int [1:58302] 0 0 2 0 0 0 0 0 0 0 ...
## ..$ SRR5567139: int [1:58302] 0 3 4 1 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 6 variables:
## ..$ SRR5567134: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567135: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567136: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567137: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567138: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5567139: 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:
## ..$ SRR5567134: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567135: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567136: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567137: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567138: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## ..$ SRR5567139: chr [1:30] "SE" "Sanger/Illumina1.9" "101" "101" ...
## $ MetadataSummary:'data.frame': 6 obs. of 7 variables:
## ..$ QC_summary : chr [1:6] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:6] "SRX2827484" "SRX2827485" "SRX2827486" "SRX2827487" ...
## ..$ SRS_accession: chr [1:6] "SRS2203352" "SRS2203353" "SRS2203354" "SRS2203355" ...
## ..$ SRP_accession: chr [1:6] "SRP107288" "SRP107288" "SRP107288" "SRP107288" ...
## ..$ Sample_name : chr [1:6] "GSM2628167" "GSM2628168" "GSM2628169" "GSM2628170" ...
## ..$ GEO_series : chr [1:6] "GSE98941" "GSE98941" "GSE98941" "GSE98941" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## $ MetadataFull :'data.frame': 6 obs. of 52 variables:
## ..$ QC_summary : chr [1:6] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:6] "SRX2827484" "SRX2827485" "SRX2827486" "SRX2827487" ...
## ..$ SRS_accession : chr [1:6] "SRS2203352" "SRS2203353" "SRS2203354" "SRS2203355" ...
## ..$ SRP_accession : chr [1:6] "SRP107288" "SRP107288" "SRP107288" "SRP107288" ...
## ..$ Sample_name : chr [1:6] "GSM2628167" "GSM2628168" "GSM2628169" "GSM2628170" ...
## ..$ GEO_series : chr [1:6] "GSE98941" "GSE98941" "GSE98941" "GSE98941" ...
## ..$ Library_name : logi [1:6] NA NA NA NA NA NA
## ..$ SampleName : chr [1:6] "GSM2628167" "GSM2628168" "GSM2628169" "GSM2628170" ...
## ..$ ReleaseDate : chr [1:6] "2018-08-02 07:04:17" "2018-08-02 07:04:17" "2018-08-02 07:04:17" "2018-08-02 07:04:17" ...
## ..$ LoadDate : chr [1:6] "2017-05-15 23:44:25" "2017-05-15 23:45:23" "2017-05-15 23:43:58" "2017-05-15 23:45:05" ...
## ..$ spots : int [1:6] 21589850 23079514 20856857 22177141 21788812 23221113
## ..$ bases : num [1:6] 2.18e+09 2.33e+09 2.11e+09 2.24e+09 2.20e+09 ...
## ..$ spots_with_mates : int [1:6] 0 0 0 0 0 0
## ..$ avgLength : int [1:6] 101 101 101 101 101 101
## ..$ size_MB : int [1:6] 634 675 610 651 638 682
## ..$ AssemblyName : logi [1:6] NA NA NA NA NA NA
## ..$ download_path : chr [1:6] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567134/SRR5567134.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567135/SRR5567135.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567136/SRR5567136.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5567137/SRR5567137.1" ...
## ..$ LibraryName : logi [1:6] NA NA NA NA NA NA
## ..$ LibraryStrategy : chr [1:6] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:6] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:6] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:6] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:6] 0 0 0 0 0 0
## ..$ InsertDev : num [1:6] 0 0 0 0 0 0
## ..$ Platform : chr [1:6] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:6] "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" "Illumina HiSeq 2500" ...
## ..$ SRAStudy : chr [1:6] "SRP107288" "SRP107288" "SRP107288" "SRP107288" ...
## ..$ BioProject : chr [1:6] "PRJNA386871" "PRJNA386871" "PRJNA386871" "PRJNA386871" ...
## ..$ Study_Pubmed_id : logi [1:6] NA NA NA NA NA NA
## ..$ ProjectID : int [1:6] 386871 386871 386871 386871 386871 386871
## ..$ Sample : chr [1:6] "SRS2203352" "SRS2203353" "SRS2203354" "SRS2203355" ...
## ..$ BioSample : chr [1:6] "SAMN07125624" "SAMN07125623" "SAMN07125622" "SAMN07125621" ...
## ..$ 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] "SRA561905" "SRA561905" "SRA561905" "SRA561905" ...
## ..$ dbgap_study_accession: logi [1:6] NA NA NA NA NA NA
## ..$ Consent : chr [1:6] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:6] "D8E078F3727DF6E48031252F936DCB47" "AC134514FCC293816E2A1D9335D06DFD" "49582B2392D2676B90444A7FD8E24F9A" "062573BAF6908A6FFC1DC9CC91FF7B42" ...
## ..$ ReadHash : chr [1:6] "7C791F4057FE6AF24AE3724D4E2F8756" "8367FE521AD98E2131DE30F3EA129659" "106E34F6B3EC46B05EE7B454F071CED9" "2C80E038816A559A31CF92C18336FE67" ...
## $ 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
## SRP102374: control basal versus cardiac fibroblasts treated with IL11: control; SRX2664166, SRX2664168, SRX2664170, SRX2664172, SRX2664174, SRX2664176, SRX2664178, SRX2664180, SRX2664182, SRX2664184: IL11; SRX2664167, SRX2664169, SRX2664171, SRX2664173, SRX2664175, SRX2664177, SRX2664179, SRX2664181, SRX2664183, SRX2664185;## 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 18 variables:
## ..$ SRR5368910: int [1:58302] 0 46 3 0 0 0 0 0 0 6 ...
## ..$ SRR5368911: int [1:58302] 0 42 7 0 0 0 0 0 0 6 ...
## ..$ SRR5368912: int [1:58302] 0 8 5 0 0 0 0 0 0 2 ...
## ..$ SRR5368913: int [1:58302] 0 16 1 0 0 0 0 0 0 2 ...
## ..$ SRR5368915: int [1:58302] 0 31 4 0 0 0 0 0 0 0 ...
## ..$ SRR5368916: int [1:58302] 0 30 5 0 0 0 0 0 0 1 ...
## ..$ SRR5368917: int [1:58302] 0 37 6 0 0 0 0 0 0 0 ...
## ..$ SRR5368918: int [1:58302] 0 22 5 0 0 0 0 0 0 6 ...
## ..$ SRR5368919: int [1:58302] 0 42 16 0 0 0 0 0 0 10 ...
## ..$ SRR5368920: int [1:58302] 0 16 1 0 0 0 0 0 0 3 ...
## ..$ SRR5368921: int [1:58302] 0 35 3 1 0 0 0 0 0 2 ...
## ..$ SRR5368922: int [1:58302] 0 10 6 0 0 0 0 0 0 0 ...
## ..$ SRR5368923: int [1:58302] 0 8 5 0 0 0 0 0 0 0 ...
## ..$ SRR5368924: int [1:58302] 0 21 1 0 0 0 0 0 0 0 ...
## ..$ SRR5368925: int [1:58302] 0 14 1 0 0 0 0 0 0 0 ...
## ..$ SRR5368926: int [1:58302] 0 18 2 0 0 0 0 0 0 0 ...
## ..$ SRR5368927: int [1:58302] 0 16 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368928: int [1:58302] 0 23 5 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 18 variables:
## ..$ SRR5368910: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368911: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368912: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368913: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368915: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368916: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368917: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368918: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368919: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368920: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368921: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368922: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368923: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368924: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368925: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368926: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368927: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368928: 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 18 variables:
## ..$ SRR5368910: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368911: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368912: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368913: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "76" ...
## ..$ SRR5368915: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368916: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "76" ...
## ..$ SRR5368917: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368918: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368919: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "76" ...
## ..$ SRR5368920: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368921: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368922: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368923: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368924: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368925: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368926: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368927: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368928: chr [1:30] "PE" "Sanger/Illumina1.9" "47" "76" ...
## $ MetadataSummary:'data.frame': 18 obs. of 7 variables:
## ..$ QC_summary : chr [1:18] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:18] "SRX2664166" "SRX2664167" "SRX2664168" "SRX2664169" ...
## ..$ SRS_accession: chr [1:18] "SRS2065947" "SRS2065948" "SRS2065949" "SRS2065950" ...
## ..$ SRP_accession: chr [1:18] "SRP102374" "SRP102374" "SRP102374" "SRP102374" ...
## ..$ Sample_name : chr [1:18] "GSM2547128" "GSM2547129" "GSM2547130" "GSM2547131" ...
## ..$ GEO_series : chr [1:18] "GSE96975" "GSE96975" "GSE96975" "GSE96975" ...
## ..$ Library_name : logi [1:18] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 18 obs. of 52 variables:
## ..$ QC_summary : chr [1:18] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:18] "SRX2664166" "SRX2664167" "SRX2664168" "SRX2664169" ...
## ..$ SRS_accession : chr [1:18] "SRS2065947" "SRS2065948" "SRS2065949" "SRS2065950" ...
## ..$ SRP_accession : chr [1:18] "SRP102374" "SRP102374" "SRP102374" "SRP102374" ...
## ..$ Sample_name : chr [1:18] "GSM2547128" "GSM2547129" "GSM2547130" "GSM2547131" ...
## ..$ GEO_series : chr [1:18] "GSE96975" "GSE96975" "GSE96975" "GSE96975" ...
## ..$ Library_name : logi [1:18] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:18] "GSM2547128" "GSM2547129" "GSM2547130" "GSM2547131" ...
## ..$ ReleaseDate : chr [1:18] "2017-11-22 17:49:40" "2017-11-22 17:49:40" "2017-11-22 17:49:40" "2017-11-22 17:49:40" ...
## ..$ LoadDate : chr [1:18] "2017-03-23 15:52:34" "2017-03-23 16:33:07" "2017-03-23 16:10:53" "2017-03-23 15:50:40" ...
## ..$ spots : int [1:18] 55404050 66728031 54731698 57993706 47741690 51931446 53391788 47344076 55336486 46340130 ...
## ..$ bases : num [1:18] 8.36e+09 1.01e+10 8.26e+09 8.75e+09 7.20e+09 ...
## ..$ spots_with_mates : int [1:18] 55404050 66728031 54731698 57993706 47741690 51931446 53391788 47344076 55336486 46340130 ...
## ..$ avgLength : int [1:18] 150 150 150 150 150 150 150 150 150 150 ...
## ..$ size_MB : int [1:18] 3475 4167 3434 3616 2972 3240 3369 2976 3479 2891 ...
## ..$ AssemblyName : logi [1:18] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:18] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368910/SRR5368910.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368911/SRR5368911.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368912/SRR5368912.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368913/SRR5368913.1" ...
## ..$ LibraryName : logi [1:18] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:18] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:18] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:18] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:18] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:18] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:18] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:18] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:18] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:18] "SRP102374" "SRP102374" "SRP102374" "SRP102374" ...
## ..$ BioProject : chr [1:18] "PRJNA380254" "PRJNA380254" "PRJNA380254" "PRJNA380254" ...
## ..$ Study_Pubmed_id : int [1:18] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:18] 380254 380254 380254 380254 380254 380254 380254 380254 380254 380254 ...
## ..$ Sample : chr [1:18] "SRS2065947" "SRS2065948" "SRS2065949" "SRS2065950" ...
## ..$ BioSample : chr [1:18] "SAMN06638169" "SAMN06638168" "SAMN06638167" "SAMN06638166" ...
## ..$ SampleType : chr [1:18] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:18] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:18] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:18] NA NA NA NA NA NA ...
## ..$ source : logi [1:18] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:18] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:18] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:18] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:18] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:18] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:18] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:18] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:18] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:18] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:18] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:18] "SRA548829" "SRA548829" "SRA548829" "SRA548829" ...
## ..$ dbgap_study_accession: logi [1:18] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:18] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:18] "2759D8A6D76E0AEAAB0BFE23BC2F61CE" "8BFA14D7C18AE81790B2B3E12CBFEC85" "0F50AF66A4D56F0B1426788BC81AEE55" "1690F53D8D696C90438CBB511FAA9CC0" ...
## ..$ ReadHash : chr [1:18] "E94156B499904838BB9ECDFBC1E9DB82" "0A62FCE193560990C0C2DCD2C2A79F76" "3A26FEA4482C4F9C38C2A1FE307A6037" "8F169860AEA0D33BD03C095253B3FD39" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 130 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP102374: control basal versus cardiac fibroblasts treated with TGFB1: control;SRX2664166, SRX2664168, SRX2664170, SRX2664172, SRX2664174, SRX2664176, SRX2664178, SRX2664180, SRX2664182, SRX2664184: TGFB1; SRX2664186, SRX2664187, SRX2664188, SRX2664189;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 12 variables:
## ..$ SRR5368910: int [1:58302] 0 46 3 0 0 0 0 0 0 6 ...
## ..$ SRR5368916: int [1:58302] 0 30 5 0 0 0 0 0 0 1 ...
## ..$ SRR5368918: int [1:58302] 0 22 5 0 0 0 0 0 0 6 ...
## ..$ SRR5368920: int [1:58302] 0 16 1 0 0 0 0 0 0 3 ...
## ..$ SRR5368922: int [1:58302] 0 10 6 0 0 0 0 0 0 0 ...
## ..$ SRR5368924: int [1:58302] 0 21 1 0 0 0 0 0 0 0 ...
## ..$ SRR5368926: int [1:58302] 0 18 2 0 0 0 0 0 0 0 ...
## ..$ SRR5368928: int [1:58302] 0 23 5 0 0 0 0 0 0 0 ...
## ..$ SRR5368930: int [1:58302] 1 17 3 0 0 0 0 0 0 0 ...
## ..$ SRR5368931: int [1:58302] 0 9 5 1 0 0 0 0 0 0 ...
## ..$ SRR5368932: int [1:58302] 0 22 2 0 0 0 0 0 0 0 ...
## ..$ SRR5368933: int [1:58302] 0 37 6 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 12 variables:
## ..$ SRR5368910: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368916: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368918: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368920: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368922: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368924: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368926: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368928: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368930: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368931: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368932: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368933: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 12 variables:
## ..$ SRR5368910: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368916: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "76" ...
## ..$ SRR5368918: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368920: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368922: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368924: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368926: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368928: chr [1:30] "PE" "Sanger/Illumina1.9" "47" "76" ...
## ..$ SRR5368930: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368931: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368932: chr [1:30] "PE" "Sanger/Illumina1.9" "48" "76" ...
## ..$ SRR5368933: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## $ MetadataSummary:'data.frame': 12 obs. of 7 variables:
## ..$ QC_summary : chr [1:12] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:12] "SRX2664166" "SRX2664172" "SRX2664174" "SRX2664176" ...
## ..$ SRS_accession: chr [1:12] "SRS2065947" "SRS2065953" "SRS2065955" "SRS2065957" ...
## ..$ SRP_accession: chr [1:12] "SRP102374" "SRP102374" "SRP102374" "SRP102374" ...
## ..$ Sample_name : chr [1:12] "GSM2547128" "GSM2547134" "GSM2547136" "GSM2547138" ...
## ..$ GEO_series : chr [1:12] "GSE96975" "GSE96975" "GSE96975" "GSE96975" ...
## ..$ Library_name : logi [1:12] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 12 obs. of 52 variables:
## ..$ QC_summary : chr [1:12] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:12] "SRX2664166" "SRX2664172" "SRX2664174" "SRX2664176" ...
## ..$ SRS_accession : chr [1:12] "SRS2065947" "SRS2065953" "SRS2065955" "SRS2065957" ...
## ..$ SRP_accession : chr [1:12] "SRP102374" "SRP102374" "SRP102374" "SRP102374" ...
## ..$ Sample_name : chr [1:12] "GSM2547128" "GSM2547134" "GSM2547136" "GSM2547138" ...
## ..$ GEO_series : chr [1:12] "GSE96975" "GSE96975" "GSE96975" "GSE96975" ...
## ..$ Library_name : logi [1:12] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:12] "GSM2547128" "GSM2547134" "GSM2547136" "GSM2547138" ...
## ..$ ReleaseDate : chr [1:12] "2017-11-22 17:49:40" "2017-11-22 17:49:40" "2017-11-22 17:49:40" "2017-11-22 17:49:40" ...
## ..$ LoadDate : chr [1:12] "2017-03-23 15:52:34" "2017-03-23 15:46:27" "2017-03-23 15:56:06" "2017-03-23 15:44:35" ...
## ..$ spots : int [1:12] 55404050 51931446 47344076 46340130 23305588 33264777 28344127 28511118 28039207 32656254 ...
## ..$ bases : num [1:12] 8.36e+09 7.84e+09 7.13e+09 6.99e+09 3.51e+09 ...
## ..$ spots_with_mates : int [1:12] 55404050 51931446 47344076 46340130 23305588 33264777 28344127 28511118 28039207 32656254 ...
## ..$ avgLength : int [1:12] 150 150 150 150 150 150 151 150 150 151 ...
## ..$ size_MB : int [1:12] 3475 3240 2976 2891 1368 1904 1630 1634 1589 1897 ...
## ..$ AssemblyName : logi [1:12] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:12] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368910/SRR5368910.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368916/SRR5368916.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368918/SRR5368918.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368920/SRR5368920.1" ...
## ..$ LibraryName : logi [1:12] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:12] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:12] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:12] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:12] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:12] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:12] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:12] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:12] "SRP102374" "SRP102374" "SRP102374" "SRP102374" ...
## ..$ BioProject : chr [1:12] "PRJNA380254" "PRJNA380254" "PRJNA380254" "PRJNA380254" ...
## ..$ Study_Pubmed_id : int [1:12] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:12] 380254 380254 380254 380254 380254 380254 380254 380254 380254 380254 ...
## ..$ Sample : chr [1:12] "SRS2065947" "SRS2065953" "SRS2065955" "SRS2065957" ...
## ..$ BioSample : chr [1:12] "SAMN06638169" "SAMN06638163" "SAMN06638161" "SAMN06638159" ...
## ..$ SampleType : chr [1:12] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:12] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:12] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:12] NA NA NA NA NA NA ...
## ..$ source : logi [1:12] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:12] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:12] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:12] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:12] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:12] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:12] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:12] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:12] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:12] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:12] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:12] "SRA548829" "SRA548829" "SRA548829" "SRA548829" ...
## ..$ dbgap_study_accession: logi [1:12] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:12] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:12] "2759D8A6D76E0AEAAB0BFE23BC2F61CE" "A9EB2DC98EA6C2B0F632F4302C24D160" "999A75AA5808D5BB0C5752AE0F8769DD" "4DE53E8EED45545091ED827EBB3B3654" ...
## ..$ ReadHash : chr [1:12] "E94156B499904838BB9ECDFBC1E9DB82" "D1CCF7945C32C82376F10AB2BB4F3CA1" "84F11306B53F3D36A06A560A5B227C2D" "9C99E2B7D0829B4FE2431ADEFE4380DB" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 330 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP102374: cardiac fibroblasts treated with IL11 versus cardiac fibroblasts treated with TGFB1: IL11; SRX2664167, SRX2664169, SRX2664171, SRX2664173, SRX2664175, SRX2664177, SRX2664179, SRX2664181, SRX2664183, SRX2664185: TGFB1; SRX2664186, SRX2664187, SRX2664188, SRX2664189;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 13 variables:
## ..$ SRR5368911: int [1:58302] 0 42 7 0 0 0 0 0 0 6 ...
## ..$ SRR5368913: int [1:58302] 0 16 1 0 0 0 0 0 0 2 ...
## ..$ SRR5368915: int [1:58302] 0 31 4 0 0 0 0 0 0 0 ...
## ..$ SRR5368917: int [1:58302] 0 37 6 0 0 0 0 0 0 0 ...
## ..$ SRR5368919: int [1:58302] 0 42 16 0 0 0 0 0 0 10 ...
## ..$ SRR5368921: int [1:58302] 0 35 3 1 0 0 0 0 0 2 ...
## ..$ SRR5368923: int [1:58302] 0 8 5 0 0 0 0 0 0 0 ...
## ..$ SRR5368925: int [1:58302] 0 14 1 0 0 0 0 0 0 0 ...
## ..$ SRR5368927: int [1:58302] 0 16 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368930: int [1:58302] 1 17 3 0 0 0 0 0 0 0 ...
## ..$ SRR5368931: int [1:58302] 0 9 5 1 0 0 0 0 0 0 ...
## ..$ SRR5368932: int [1:58302] 0 22 2 0 0 0 0 0 0 0 ...
## ..$ SRR5368933: int [1:58302] 0 37 6 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 13 variables:
## ..$ SRR5368911: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368913: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368915: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368917: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368919: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368921: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368923: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368925: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368927: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368930: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368931: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368932: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5368933: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 13 variables:
## ..$ SRR5368911: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368913: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "76" ...
## ..$ SRR5368915: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368917: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368919: chr [1:30] "PE" "Sanger/Illumina1.9" "51" "76" ...
## ..$ SRR5368921: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368923: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368925: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368927: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368930: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368931: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## ..$ SRR5368932: chr [1:30] "PE" "Sanger/Illumina1.9" "48" "76" ...
## ..$ SRR5368933: chr [1:30] "PE" "Sanger/Illumina1.9" "35" "76" ...
## $ MetadataSummary:'data.frame': 13 obs. of 7 variables:
## ..$ QC_summary : chr [1:13] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession: chr [1:13] "SRX2664167" "SRX2664169" "SRX2664171" "SRX2664173" ...
## ..$ SRS_accession: chr [1:13] "SRS2065948" "SRS2065950" "SRS2065952" "SRS2065954" ...
## ..$ SRP_accession: chr [1:13] "SRP102374" "SRP102374" "SRP102374" "SRP102374" ...
## ..$ Sample_name : chr [1:13] "GSM2547129" "GSM2547131" "GSM2547133" "GSM2547135" ...
## ..$ GEO_series : chr [1:13] "GSE96975" "GSE96975" "GSE96975" "GSE96975" ...
## ..$ Library_name : logi [1:13] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 13 obs. of 52 variables:
## ..$ QC_summary : chr [1:13] "WARN(8)" "WARN(8)" "WARN(8)" "WARN(8)" ...
## ..$ SRX_accession : chr [1:13] "SRX2664167" "SRX2664169" "SRX2664171" "SRX2664173" ...
## ..$ SRS_accession : chr [1:13] "SRS2065948" "SRS2065950" "SRS2065952" "SRS2065954" ...
## ..$ SRP_accession : chr [1:13] "SRP102374" "SRP102374" "SRP102374" "SRP102374" ...
## ..$ Sample_name : chr [1:13] "GSM2547129" "GSM2547131" "GSM2547133" "GSM2547135" ...
## ..$ GEO_series : chr [1:13] "GSE96975" "GSE96975" "GSE96975" "GSE96975" ...
## ..$ Library_name : logi [1:13] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:13] "GSM2547129" "GSM2547131" "GSM2547133" "GSM2547135" ...
## ..$ ReleaseDate : chr [1:13] "2017-11-22 17:49:40" "2017-11-22 17:49:40" "2017-11-22 17:49:40" "2017-11-22 17:49:40" ...
## ..$ LoadDate : chr [1:13] "2017-03-23 16:33:07" "2017-03-23 15:50:40" "2017-03-23 15:47:03" "2017-03-23 15:49:48" ...
## ..$ spots : int [1:13] 66728031 57993706 47741690 53391788 55336486 51736843 27034010 29197005 27300769 28039207 ...
## ..$ bases : num [1:13] 1.01e+10 8.75e+09 7.20e+09 8.06e+09 8.35e+09 ...
## ..$ spots_with_mates : int [1:13] 66728031 57993706 47741690 53391788 55336486 51736843 27034010 29197005 27300769 28039207 ...
## ..$ avgLength : int [1:13] 150 150 150 150 150 150 150 151 151 150 ...
## ..$ size_MB : int [1:13] 4167 3616 2972 3369 3479 3227 1558 1668 1559 1589 ...
## ..$ AssemblyName : logi [1:13] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:13] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368911/SRR5368911.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368913/SRR5368913.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368915/SRR5368915.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR5368917/SRR5368917.1" ...
## ..$ LibraryName : logi [1:13] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:13] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:13] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:13] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:13] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:13] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:13] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:13] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:13] "SRP102374" "SRP102374" "SRP102374" "SRP102374" ...
## ..$ BioProject : chr [1:13] "PRJNA380254" "PRJNA380254" "PRJNA380254" "PRJNA380254" ...
## ..$ Study_Pubmed_id : int [1:13] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:13] 380254 380254 380254 380254 380254 380254 380254 380254 380254 380254 ...
## ..$ Sample : chr [1:13] "SRS2065948" "SRS2065950" "SRS2065952" "SRS2065954" ...
## ..$ BioSample : chr [1:13] "SAMN06638168" "SAMN06638166" "SAMN06638164" "SAMN06638162" ...
## ..$ SampleType : chr [1:13] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:13] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:13] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:13] NA NA NA NA NA NA ...
## ..$ source : logi [1:13] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:13] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:13] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:13] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:13] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:13] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:13] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:13] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:13] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:13] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:13] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:13] "SRA548829" "SRA548829" "SRA548829" "SRA548829" ...
## ..$ dbgap_study_accession: logi [1:13] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:13] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:13] "8BFA14D7C18AE81790B2B3E12CBFEC85" "1690F53D8D696C90438CBB511FAA9CC0" "989FFA87BF5FCBCFB3A09CAC99215E88" "6408208E2437C4D07F644374C7546DF0" ...
## ..$ ReadHash : chr [1:13] "0A62FCE193560990C0C2DCD2C2A79F76" "8F169860AEA0D33BD03C095253B3FD39" "E33DCECCC5E59062EEF8FBB3AC22A53F" "D0D611B60A617EC8C7E3EDBFC5988360" ...
## $ absent : chr(0)## converting counts to integer mode## using supplied model matrix## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 240 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing
## SRP100748: human induced pluripotent stem cells (hiPSCs) versus DMSO treated hiPSCs: hiPSCs; SRX2592092, SRX2592093, SRX2592094, SRX2592095: DMSO; SRX2592100, SRX2592101, SRX2592102, SRX2592103;## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 23 variables:
## ..$ SRR5289322: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289323: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289324: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289325: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289326: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289327: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289328: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289329: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289346: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289347: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289348: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289349: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289350: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289351: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289352: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289353: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289354: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289355: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289357: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289358: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289359: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289360: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289361: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 23 variables:
## ..$ SRR5289322: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289323: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289324: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289325: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289326: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289327: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289328: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289329: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289346: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289347: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289348: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289349: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289350: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289351: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289352: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289353: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289354: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289355: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289357: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289358: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289359: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289360: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289361: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 23 variables:
## ..$ SRR5289322: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289323: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289324: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289325: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289326: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289327: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289328: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289329: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289346: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289347: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289348: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289349: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289350: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289351: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289352: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289353: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289354: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289355: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289357: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289358: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289359: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289360: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289361: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## $ MetadataSummary:'data.frame': 23 obs. of 7 variables:
## ..$ QC_summary : chr [1:23] "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 [1:23] "SRX2592094" "SRX2592094" "SRX2592094" "SRX2592094" ...
## ..$ SRS_accession: chr [1:23] "SRS2020304" "SRS2020304" "SRS2020304" "SRS2020304" ...
## ..$ SRP_accession: chr [1:23] "SRP100748" "SRP100748" "SRP100748" "SRP100748" ...
## ..$ Sample_name : chr [1:23] "GSM2509702" "GSM2509702" "GSM2509702" "GSM2509702" ...
## ..$ GEO_series : chr [1:23] "GSE95390" "GSE95390" "GSE95390" "GSE95390" ...
## ..$ Library_name : logi [1:23] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 23 obs. of 52 variables:
## ..$ QC_summary : chr [1:23] "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" "FAIL(3,4,5,6,7)" ...
## ..$ SRX_accession : chr [1:23] "SRX2592094" "SRX2592094" "SRX2592094" "SRX2592094" ...
## ..$ SRS_accession : chr [1:23] "SRS2020304" "SRS2020304" "SRS2020304" "SRS2020304" ...
## ..$ SRP_accession : chr [1:23] "SRP100748" "SRP100748" "SRP100748" "SRP100748" ...
## ..$ Sample_name : chr [1:23] "GSM2509702" "GSM2509702" "GSM2509702" "GSM2509702" ...
## ..$ GEO_series : chr [1:23] "GSE95390" "GSE95390" "GSE95390" "GSE95390" ...
## ..$ Library_name : logi [1:23] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:23] "GSM2509702" "GSM2509702" "GSM2509702" "GSM2509702" ...
## ..$ ReleaseDate : chr [1:23] "2018-01-02 09:24:05" "2018-01-02 09:24:05" "2018-01-02 09:24:05" "2018-01-02 09:24:05" ...
## ..$ LoadDate : chr [1:23] "2017-02-27 09:28:29" "2017-02-27 09:28:30" "2017-02-27 09:28:34" "2017-02-27 09:28:31" ...
## ..$ spots : int [1:23] 3726818 3484836 3831642 3666119 3836924 3582091 3931165 3783910 3775327 3528735 ...
## ..$ bases : int [1:23] 134165448 125454096 137939112 131980284 138129264 128955276 141521940 136220760 135911772 127034460 ...
## ..$ spots_with_mates : int [1:23] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:23] 36 36 36 36 36 36 36 36 36 36 ...
## ..$ size_MB : int [1:23] 38 35 39 37 39 36 39 38 38 35 ...
## ..$ AssemblyName : logi [1:23] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:23] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289322/SRR5289322.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289323/SRR5289323.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289324/SRR5289324.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289325/SRR5289325.1" ...
## ..$ LibraryName : logi [1:23] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:23] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" ...
## ..$ LibrarySelection : chr [1:23] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ LibrarySource : chr [1:23] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:23] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:23] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:23] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:23] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:23] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:23] "SRP100748" "SRP100748" "SRP100748" "SRP100748" ...
## ..$ BioProject : chr [1:23] "PRJNA376872" "PRJNA376872" "PRJNA376872" "PRJNA376872" ...
## ..$ Study_Pubmed_id : logi [1:23] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:23] 376872 376872 376872 376872 376872 376872 376872 376872 376872 376872 ...
## ..$ Sample : chr [1:23] "SRS2020304" "SRS2020304" "SRS2020304" "SRS2020304" ...
## ..$ BioSample : chr [1:23] "SAMN06472403" "SAMN06472403" "SAMN06472403" "SAMN06472403" ...
## ..$ SampleType : chr [1:23] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:23] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:23] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:23] NA NA NA NA NA NA ...
## ..$ source : logi [1:23] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:23] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:23] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:23] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:23] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:23] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:23] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:23] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:23] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:23] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:23] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:23] "SRA540492" "SRA540492" "SRA540492" "SRA540492" ...
## ..$ dbgap_study_accession: logi [1:23] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:23] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:23] "8C87893BE60CB36ADAB3D0E03E3B9C11" "0ABC760E0BC6AF2FD7059957672D155F" "558C2D74CB4B98E4329209ED298759AF" "A8CAFD27B5ACE009E1EEBE18D221F404" ...
## ..$ ReadHash : chr [1:23] "E79E2BD3F7424091E209DF14D9518FEE" "48ABA26815A92E9DEFBC11BDAF5BD0B7" "0C7F743098BC8B8A483CACA44987C8B7" "7814B6C8F5CEA4FD9E7AF2C5FB171AC9" ...
## $ absent : chr(0)## SRP100748: human induced pluripotent stem cells(hiPSCs) versus ISX-9 treated hiPSCs: hiPSCs; SRX2592092, SRX2592093, SRX2592094, SRX2592095: ISX-9; SRX2592096, SRX2592097, SRX2592098, SRX2592099;
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 28 variables:
## ..$ SRR5289314: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289315: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289316: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289317: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289322: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289323: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289324: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289325: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289326: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289327: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289328: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289329: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289330: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289331: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289332: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289333: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289334: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289335: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289336: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289337: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289338: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289339: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289340: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289341: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289342: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289343: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289344: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289345: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 28 variables:
## ..$ SRR5289314: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289315: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289316: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289317: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289322: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289323: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289324: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289325: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289326: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289327: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289328: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289329: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289330: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289331: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289332: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289333: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289334: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289335: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289336: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289337: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289338: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289339: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289340: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289341: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289342: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289343: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289344: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289345: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## $ GeneInfo :'data.frame': 58302 obs. of 5 variables:
## ..$ GeneSymbol : chr [1:58302] "DDX11L1" "WASH7P" "MIR6859-1" "MIR1302-2HG" ...
## ..$ mean : int [1:58302] 973 1351 68 641 138 948 840 1295 2227 1082 ...
## ..$ median : int [1:58302] 632 1351 68 712 138 1187 840 1414 2618 629 ...
## ..$ longest_isoform: int [1:58302] 1657 1351 68 712 138 1187 840 1414 2618 2748 ...
## ..$ merged : int [1:58302] 1735 1351 68 1021 138 1219 840 1414 2618 3726 ...
## $ TxInfo :'data.frame': 180869 obs. of 3 variables:
## ..$ GeneID : chr [1:180869] "ENSG00000237235.2" "ENSG00000228985.1" "ENSG00000223997.1" "ENSG00000282253.1" ...
## ..$ GeneSymbol: chr [1:180869] "TRDD2" "TRDD3" "TRDD1" "AC239618.6" ...
## ..$ TxLength : int [1:180869] 9 13 8 12 12 17 20 19 16 18 ...
## $ QcMx :'data.frame': 30 obs. of 28 variables:
## ..$ SRR5289314: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289315: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289316: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289317: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289322: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289323: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289324: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289325: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289326: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289327: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289328: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289329: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289330: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289331: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289332: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289333: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289334: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289335: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289336: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289337: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289338: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289339: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289340: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289341: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289342: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289343: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289344: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289345: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## $ MetadataSummary:'data.frame': 28 obs. of 7 variables:
## ..$ QC_summary : chr [1:28] "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 [1:28] "SRX2592092" "SRX2592092" "SRX2592092" "SRX2592092" ...
## ..$ SRS_accession: chr [1:28] "SRS2020302" "SRS2020302" "SRS2020302" "SRS2020302" ...
## ..$ SRP_accession: chr [1:28] "SRP100748" "SRP100748" "SRP100748" "SRP100748" ...
## ..$ Sample_name : chr [1:28] "GSM2509700" "GSM2509700" "GSM2509700" "GSM2509700" ...
## ..$ GEO_series : chr [1:28] "GSE95390" "GSE95390" "GSE95390" "GSE95390" ...
## ..$ Library_name : logi [1:28] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 28 obs. of 52 variables:
## ..$ QC_summary : chr [1:28] "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 [1:28] "SRX2592092" "SRX2592092" "SRX2592092" "SRX2592092" ...
## ..$ SRS_accession : chr [1:28] "SRS2020302" "SRS2020302" "SRS2020302" "SRS2020302" ...
## ..$ SRP_accession : chr [1:28] "SRP100748" "SRP100748" "SRP100748" "SRP100748" ...
## ..$ Sample_name : chr [1:28] "GSM2509700" "GSM2509700" "GSM2509700" "GSM2509700" ...
## ..$ GEO_series : chr [1:28] "GSE95390" "GSE95390" "GSE95390" "GSE95390" ...
## ..$ Library_name : logi [1:28] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:28] "GSM2509700" "GSM2509700" "GSM2509700" "GSM2509700" ...
## ..$ ReleaseDate : chr [1:28] "2018-01-02 09:24:05" "2018-01-02 09:24:05" "2018-01-02 09:24:05" "2018-01-02 09:24:05" ...
## ..$ LoadDate : chr [1:28] "2017-02-27 09:27:15" "2017-02-27 09:27:15" "2017-02-27 09:28:06" "2017-02-27 09:27:26" ...
## ..$ spots : int [1:28] 3805777 3560465 3903676 3731156 3726818 3484836 3831642 3666119 3836924 3582091 ...
## ..$ bases : int [1:28] 137007972 128176740 140532336 134321616 134165448 125454096 137939112 131980284 138129264 128955276 ...
## ..$ spots_with_mates : int [1:28] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:28] 36 36 36 36 36 36 36 36 36 36 ...
## ..$ size_MB : int [1:28] 38 35 39 37 38 35 39 37 39 36 ...
## ..$ AssemblyName : logi [1:28] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:28] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289314/SRR5289314.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289315/SRR5289315.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289316/SRR5289316.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289317/SRR5289317.1" ...
## ..$ LibraryName : logi [1:28] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:28] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" ...
## ..$ LibrarySelection : chr [1:28] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ LibrarySource : chr [1:28] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:28] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:28] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:28] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:28] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:28] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:28] "SRP100748" "SRP100748" "SRP100748" "SRP100748" ...
## ..$ BioProject : chr [1:28] "PRJNA376872" "PRJNA376872" "PRJNA376872" "PRJNA376872" ...
## ..$ Study_Pubmed_id : logi [1:28] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:28] 376872 376872 376872 376872 376872 376872 376872 376872 376872 376872 ...
## ..$ Sample : chr [1:28] "SRS2020302" "SRS2020302" "SRS2020302" "SRS2020302" ...
## ..$ BioSample : chr [1:28] "SAMN06472408" "SAMN06472408" "SAMN06472408" "SAMN06472408" ...
## ..$ SampleType : chr [1:28] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:28] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:28] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:28] NA NA NA NA NA NA ...
## ..$ source : logi [1:28] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:28] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:28] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:28] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:28] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:28] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:28] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:28] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:28] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:28] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:28] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:28] "SRA540492" "SRA540492" "SRA540492" "SRA540492" ...
## ..$ dbgap_study_accession: logi [1:28] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:28] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:28] "3CF3FD26714F97452754E6833F794A9C" "9E2148C19914D5E60B4F037D6322A7E4" "D29279BF2D8C1672B6A0F238ABE1B89E" "D06AED70D49DCFC36C3100AD6E7D854F" ...
## ..$ ReadHash : chr [1:28] "B075A418B83A2EEE93027DAA412BE9E3" "6A9FB3701D572463EFA6EF5C3C4FF48F" "A22558B20A5293BABAEEEB7E1411D922" "C49DC1D3789D7C9A7D0C64E019533BD0" ...
## $ absent : chr(0)## SRP100748: DMSO treated hiPSCs versus ISX-9 treated hiPSCs: DMSO; SRX2592100, SRX2592101, SRX2592102, SRX2592103: ISX-9; SRX2592096, SRX2592097, SRX2592098, SRX2592099;
## 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 31 variables:
## ..$ SRR5289330: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289331: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289332: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289333: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289334: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289335: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289336: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289337: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289338: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289339: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289340: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289341: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289342: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289343: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289344: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289345: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289346: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289347: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289348: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289349: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289350: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289351: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289352: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289353: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289354: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289355: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289357: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289358: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289359: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289360: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289361: int [1:58302] 0 0 0 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 31 variables:
## ..$ SRR5289330: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289331: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289332: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289333: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289334: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289335: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289336: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289337: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289338: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289339: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289340: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289341: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289342: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289343: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289344: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289345: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289346: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289347: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289348: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289349: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289350: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289351: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289352: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289353: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289354: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289355: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289357: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289358: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289359: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289360: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5289361: 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 31 variables:
## ..$ SRR5289330: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289331: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289332: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289333: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289334: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289335: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289336: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289337: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289338: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289339: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289340: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289341: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289342: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289343: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289344: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289345: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289346: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289347: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289348: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289349: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289350: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289351: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289352: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289353: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289354: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289355: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289357: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289358: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289359: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289360: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## ..$ SRR5289361: chr [1:30] "SE" "Sanger/Illumina1.9" "36" "36" ...
## $ MetadataSummary:'data.frame': 31 obs. of 7 variables:
## ..$ QC_summary : chr [1:31] "FAIL(4,6,7)" "FAIL(4,5,6,7)" "FAIL(4,6,7)" "FAIL(4,6,7)" ...
## ..$ SRX_accession: chr [1:31] "SRX2592096" "SRX2592096" "SRX2592096" "SRX2592096" ...
## ..$ SRS_accession: chr [1:31] "SRS2020305" "SRS2020305" "SRS2020305" "SRS2020305" ...
## ..$ SRP_accession: chr [1:31] "SRP100748" "SRP100748" "SRP100748" "SRP100748" ...
## ..$ Sample_name : chr [1:31] "GSM2509704" "GSM2509704" "GSM2509704" "GSM2509704" ...
## ..$ GEO_series : chr [1:31] "GSE95390" "GSE95390" "GSE95390" "GSE95390" ...
## ..$ Library_name : logi [1:31] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 31 obs. of 52 variables:
## ..$ QC_summary : chr [1:31] "FAIL(4,6,7)" "FAIL(4,5,6,7)" "FAIL(4,6,7)" "FAIL(4,6,7)" ...
## ..$ SRX_accession : chr [1:31] "SRX2592096" "SRX2592096" "SRX2592096" "SRX2592096" ...
## ..$ SRS_accession : chr [1:31] "SRS2020305" "SRS2020305" "SRS2020305" "SRS2020305" ...
## ..$ SRP_accession : chr [1:31] "SRP100748" "SRP100748" "SRP100748" "SRP100748" ...
## ..$ Sample_name : chr [1:31] "GSM2509704" "GSM2509704" "GSM2509704" "GSM2509704" ...
## ..$ GEO_series : chr [1:31] "GSE95390" "GSE95390" "GSE95390" "GSE95390" ...
## ..$ Library_name : logi [1:31] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:31] "GSM2509704" "GSM2509704" "GSM2509704" "GSM2509704" ...
## ..$ ReleaseDate : chr [1:31] "2018-01-02 09:24:05" "2018-01-02 09:24:05" "2018-01-02 09:24:05" "2018-01-02 09:24:05" ...
## ..$ LoadDate : chr [1:31] "2017-02-27 09:28:57" "2017-02-27 09:28:40" "2017-02-27 09:29:11" "2017-02-27 09:28:46" ...
## ..$ spots : int [1:31] 4376083 4131161 4486051 4337656 4172994 3918553 4285832 4127659 4329697 4076131 ...
## ..$ bases : int [1:31] 157538988 148721796 161497836 156155616 150227784 141067908 154289952 148595724 155869092 146740716 ...
## ..$ spots_with_mates : int [1:31] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ avgLength : int [1:31] 36 36 36 36 36 36 36 36 36 36 ...
## ..$ size_MB : int [1:31] 44 41 44 43 42 39 43 41 43 40 ...
## ..$ AssemblyName : logi [1:31] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:31] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289330/SRR5289330.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289331/SRR5289331.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289332/SRR5289332.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5289333/SRR5289333.1" ...
## ..$ LibraryName : logi [1:31] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:31] "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" "miRNA-Seq" ...
## ..$ LibrarySelection : chr [1:31] "size fractionation" "size fractionation" "size fractionation" "size fractionation" ...
## ..$ LibrarySource : chr [1:31] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:31] "SINGLE" "SINGLE" "SINGLE" "SINGLE" ...
## ..$ InsertSize : int [1:31] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:31] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:31] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:31] "NextSeq 500" "NextSeq 500" "NextSeq 500" "NextSeq 500" ...
## ..$ SRAStudy : chr [1:31] "SRP100748" "SRP100748" "SRP100748" "SRP100748" ...
## ..$ BioProject : chr [1:31] "PRJNA376872" "PRJNA376872" "PRJNA376872" "PRJNA376872" ...
## ..$ Study_Pubmed_id : logi [1:31] NA NA NA NA NA NA ...
## ..$ ProjectID : int [1:31] 376872 376872 376872 376872 376872 376872 376872 376872 376872 376872 ...
## ..$ Sample : chr [1:31] "SRS2020305" "SRS2020305" "SRS2020305" "SRS2020305" ...
## ..$ BioSample : chr [1:31] "SAMN06472399" "SAMN06472399" "SAMN06472399" "SAMN06472399" ...
## ..$ SampleType : chr [1:31] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:31] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:31] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:31] NA NA NA NA NA NA ...
## ..$ source : logi [1:31] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:31] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:31] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:31] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:31] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:31] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:31] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:31] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:31] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:31] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:31] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:31] "SRA540492" "SRA540492" "SRA540492" "SRA540492" ...
## ..$ dbgap_study_accession: logi [1:31] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:31] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:31] "A22CE25A7E33F77015ADCDFCBA259272" "F3E4B2449C6281AB84E67E65E50E70F1" "0343C9AB9E72EB9C95AE5A3F7705F50A" "1E0E875FBEB90CD6A691954F2351C5C7" ...
## ..$ ReadHash : chr [1:31] "F62162E2BE589382919113379C034A0F" "1AB55D70C71391B22EB89235392F0696" "5B033A14E5B6748E6A504C1801A94428" "4229D51AB04F3B1F24C3211306DA3097" ...
## $ absent : chr(0)## SRP100426: control vs cardiac stromal cells from arrhythmogenic cardiomyopathy patients (ACM): control; SRX2578750, SRX2578751, SRX2578752: ACM; SRX2578747, SRX2578748, SRX2578749; sex
## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
## List of 8
## $ GeneCounts :'data.frame': 58302 obs. of 21 variables:
## ..$ SRR5274775: int [1:58302] 0 9 1 0 0 0 0 0 0 0 ...
## ..$ SRR5274776: int [1:58302] 0 10 1 0 0 0 0 0 0 0 ...
## ..$ SRR5274777: int [1:58302] 0 7 0 1 0 0 0 0 0 0 ...
## ..$ SRR5274778: int [1:58302] 0 6 1 1 0 0 0 0 0 0 ...
## ..$ SRR5274779: int [1:58302] 0 5 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274780: int [1:58302] 0 8 1 1 0 0 0 0 0 1 ...
## ..$ SRR5274781: int [1:58302] 0 19 2 0 0 0 0 0 0 0 ...
## ..$ SRR5274782: int [1:58302] 0 9 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274783: int [1:58302] 0 16 1 0 0 0 0 0 0 0 ...
## ..$ SRR5274784: int [1:58302] 0 15 1 0 0 0 0 0 0 0 ...
## ..$ SRR5274785: int [1:58302] 0 9 1 0 0 0 0 0 0 0 ...
## ..$ SRR5274786: int [1:58302] 0 9 2 0 0 0 0 0 0 1 ...
## ..$ SRR5274787: int [1:58302] 0 5 1 0 0 0 0 0 0 0 ...
## ..$ SRR5274788: int [1:58302] 0 3 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274789: int [1:58302] 0 12 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274790: int [1:58302] 0 8 2 1 0 0 0 0 0 0 ...
## ..$ SRR5274791: int [1:58302] 0 13 1 0 0 0 0 0 0 0 ...
## ..$ SRR5274792: int [1:58302] 1 13 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274793: int [1:58302] 0 15 1 0 0 0 0 0 0 0 ...
## ..$ SRR5274794: int [1:58302] 0 13 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274796: int [1:58302] 1 18 2 0 0 0 0 0 0 0 ...
## $ TxCounts :'data.frame': 180869 obs. of 21 variables:
## ..$ SRR5274775: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274776: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274777: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274778: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274779: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274780: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274781: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274782: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274783: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274784: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274785: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274786: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274787: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274788: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274789: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274790: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274791: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274792: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274793: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274794: num [1:180869] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ SRR5274796: 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 21 variables:
## ..$ SRR5274775: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274776: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274777: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274778: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274779: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274780: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274781: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274782: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274783: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274784: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274785: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274786: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274787: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274788: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274789: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274790: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274791: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274792: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274793: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274794: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## ..$ SRR5274796: chr [1:30] "PE" "Sanger/Illumina1.9" "100" "100" ...
## $ MetadataSummary:'data.frame': 21 obs. of 7 variables:
## ..$ QC_summary : chr [1:21] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession: chr [1:21] "SRX2578747" "SRX2578747" "SRX2578748" "SRX2578748" ...
## ..$ SRS_accession: chr [1:21] "SRS1993358" "SRS1993358" "SRS1993361" "SRS1993361" ...
## ..$ SRP_accession: chr [1:21] "SRP100426" "SRP100426" "SRP100426" "SRP100426" ...
## ..$ Sample_name : chr [1:21] "GSM2496457" "GSM2496457" "GSM2496458" "GSM2496458" ...
## ..$ GEO_series : chr [1:21] "GSE95120" "GSE95120" "GSE95120" "GSE95120" ...
## ..$ Library_name : logi [1:21] NA NA NA NA NA NA ...
## $ MetadataFull :'data.frame': 21 obs. of 52 variables:
## ..$ QC_summary : chr [1:21] "PASS" "PASS" "PASS" "PASS" ...
## ..$ SRX_accession : chr [1:21] "SRX2578747" "SRX2578747" "SRX2578748" "SRX2578748" ...
## ..$ SRS_accession : chr [1:21] "SRS1993358" "SRS1993358" "SRS1993361" "SRS1993361" ...
## ..$ SRP_accession : chr [1:21] "SRP100426" "SRP100426" "SRP100426" "SRP100426" ...
## ..$ Sample_name : chr [1:21] "GSM2496457" "GSM2496457" "GSM2496458" "GSM2496458" ...
## ..$ GEO_series : chr [1:21] "GSE95120" "GSE95120" "GSE95120" "GSE95120" ...
## ..$ Library_name : logi [1:21] NA NA NA NA NA NA ...
## ..$ SampleName : chr [1:21] "GSM2496457" "GSM2496457" "GSM2496458" "GSM2496458" ...
## ..$ ReleaseDate : chr [1:21] "2018-06-27 17:10:06" "2018-06-27 17:10:06" "2018-06-27 17:10:06" "2018-06-27 17:10:06" ...
## ..$ LoadDate : chr [1:21] "2017-02-21 10:05:50" "2017-02-21 10:06:42" "2017-02-21 10:04:16" "2017-02-21 10:06:43" ...
## ..$ spots : int [1:21] 18696276 20394271 14820785 15234559 12634459 13777743 19084119 19619923 16257587 17751966 ...
## ..$ bases : num [1:21] 3.74e+09 4.08e+09 2.96e+09 3.05e+09 2.53e+09 ...
## ..$ spots_with_mates : int [1:21] 18696276 20394271 14820785 15234559 12634459 13777743 19084119 19619923 16257587 17751966 ...
## ..$ avgLength : int [1:21] 200 200 200 200 200 200 200 200 200 200 ...
## ..$ size_MB : int [1:21] 1572 1709 1240 1269 1063 1155 1610 1648 1378 1500 ...
## ..$ AssemblyName : logi [1:21] NA NA NA NA NA NA ...
## ..$ download_path : chr [1:21] "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5274775/SRR5274775.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5274776/SRR5274776.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5274777/SRR5274777.1" "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-9/SRR5274778/SRR5274778.1" ...
## ..$ LibraryName : logi [1:21] NA NA NA NA NA NA ...
## ..$ LibraryStrategy : chr [1:21] "RNA-Seq" "RNA-Seq" "RNA-Seq" "RNA-Seq" ...
## ..$ LibrarySelection : chr [1:21] "cDNA" "cDNA" "cDNA" "cDNA" ...
## ..$ LibrarySource : chr [1:21] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" "TRANSCRIPTOMIC" ...
## ..$ LibraryLayout : chr [1:21] "PAIRED" "PAIRED" "PAIRED" "PAIRED" ...
## ..$ InsertSize : int [1:21] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ InsertDev : num [1:21] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ Platform : chr [1:21] "ILLUMINA" "ILLUMINA" "ILLUMINA" "ILLUMINA" ...
## ..$ Model : chr [1:21] "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" "Illumina HiSeq 2000" ...
## ..$ SRAStudy : chr [1:21] "SRP100426" "SRP100426" "SRP100426" "SRP100426" ...
## ..$ BioProject : chr [1:21] "PRJNA376124" "PRJNA376124" "PRJNA376124" "PRJNA376124" ...
## ..$ Study_Pubmed_id : int [1:21] 2 2 2 2 2 2 2 2 2 2 ...
## ..$ ProjectID : int [1:21] 376124 376124 376124 376124 376124 376124 376124 376124 376124 376124 ...
## ..$ Sample : chr [1:21] "SRS1993358" "SRS1993358" "SRS1993361" "SRS1993361" ...
## ..$ BioSample : chr [1:21] "SAMN06350659" "SAMN06350659" "SAMN06350658" "SAMN06350658" ...
## ..$ SampleType : chr [1:21] "simple" "simple" "simple" "simple" ...
## ..$ TaxID : int [1:21] 9606 9606 9606 9606 9606 9606 9606 9606 9606 9606 ...
## ..$ ScientificName : chr [1:21] "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
## ..$ g1k_pop_code : logi [1:21] NA NA NA NA NA NA ...
## ..$ source : logi [1:21] NA NA NA NA NA NA ...
## ..$ g1k_analysis_group : logi [1:21] NA NA NA NA NA NA ...
## ..$ Subject_ID : logi [1:21] NA NA NA NA NA NA ...
## ..$ Sex : logi [1:21] NA NA NA NA NA NA ...
## ..$ Disease : logi [1:21] NA NA NA NA NA NA ...
## ..$ Tumor : chr [1:21] "no" "no" "no" "no" ...
## ..$ Affection_Status : logi [1:21] NA NA NA NA NA NA ...
## ..$ Analyte_Type : logi [1:21] NA NA NA NA NA NA ...
## ..$ Histological_Type : logi [1:21] NA NA NA NA NA NA ...
## ..$ Body_Site : logi [1:21] NA NA NA NA NA NA ...
## ..$ CenterName : chr [1:21] "GEO" "GEO" "GEO" "GEO" ...
## ..$ Submission : chr [1:21] "SRA539172" "SRA539172" "SRA539172" "SRA539172" ...
## ..$ dbgap_study_accession: logi [1:21] NA NA NA NA NA NA ...
## ..$ Consent : chr [1:21] "public" "public" "public" "public" ...
## ..$ RunHash : chr [1:21] "E66A022EEAB3B046D5D92DEAAC1EC464" "7C52F196C80936D0DBE2C77236859E37" "99079DB4A132FDE98BC18C434714EB6B" "73959829607601FA1B7E373FFA9C70FA" ...
## ..$ ReadHash : chr [1:21] "2BFA707F8F4D3A0FE6BD547ABE615C89" "DA92A7AD2C1242EE0E7DC9DA19E35228" "6DD54A2556346F578590EE6C71215368" "0E28929C0102D05B7EC178A4666ED14F" ...
## $ 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
lapply(data,length)## [[1]]
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## [1] 8data <- data[which(lapply(data,length)>1)]
data <- data[which(lapply(data,function(x) length(x[[5]] ))>0)]
saveRDS(data,"heartdisease_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)$class <- "GMT"
write.GMT(gs,"heartdisease_ensemblIDs.gmt")
gs1 <- lapply(data, function(x) { x[7] })
gs2 <- lapply(data, function(x) { x[8] })
gs <- c(gs1,gs2)
gs <- lapply(gs,function(x) x[[1]] )
gs <- lapply(gs,function(x) { x[[3]] <- unique(x[[3]] ) ; return(x) } )
attributes(gs)$class <- "GMT"
write.GMT(gs,"heartdisease_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