Mercurial > repos > sblanck > smagexp
diff Recount.R @ 34:0a74b8de4c10 draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 288d0dce1c0877bf9c3431a581d638b0ac336d3f
| author | sblanck |
|---|---|
| date | Thu, 21 Jun 2018 10:41:50 -0400 |
| parents | 2d7595c8041d |
| children |
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--- a/Recount.R Thu Jun 21 10:06:23 2018 -0400 +++ b/Recount.R Thu Jun 21 10:41:50 2018 -0400 @@ -23,7 +23,7 @@ } #loading libraries -suppressPackageStartupMessages(require(GEOquery)) +suppressPackageStartupMessages(require(recount)) studyID=opt$id reportFile=opt$report @@ -40,8 +40,8 @@ { currentCount=as.data.frame(counts[,i]) sampleID=colnames(counts)[i] - colnames(currentCount)=sampleID - write.table(x=currentCount,file=paste0("./split/",sampleID,"_",conditions[i]),sep="\t",row.names = T, col.names = T) + #colnames(currentCount)=sampleID + write.table(x=currentCount,file=paste0("./split/",sampleID,"_",conditions[i],'.tabular'),sep="\t",row.names = T, col.names = F) } -write.table(as.data.frame(cbind(sampleID=colnames(counts),title=conditions)),quote = FALSE,col.names =TRUE, row.names=FALSE,file=reportFile,sep="\t") \ No newline at end of file +write.table(as.data.frame(cbind(sampleID=colnames(counts),title=conditions)),quote = FALSE,col.names =TRUE, row.names=FALSE,file=reportFile,sep="\t")