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