diff --git a/workflow/scripts/convertGeneSymbols.R b/workflow/scripts/convertGeneSymbols.R index 7b05b92e5d251050a78e7f546aa8b042d994c623..452f450d79bd2928fa5a26acc36569b8fbfd1572 100644 --- a/workflow/scripts/convertGeneSymbols.R +++ b/workflow/scripts/convertGeneSymbols.R @@ -10,6 +10,9 @@ rm(option_list) countTable <- read.csv(paste0(opt$repRID,".countData.countTable.csv"), stringsAsFactors=FALSE) geneID <- read.delim("geneID.tsv", header=FALSE, stringsAsFactors=FALSE) Entrez <- read.delim("Entrez.tsv", header=FALSE, stringsAsFactors=FALSE) +convert <- merge(x=Entrex,y=geneID,by.x="V1",by.y="V1",all.x=TRUE) + + convert <- data.frame(geneID=countTable$Geneid) convert <- merge(x=convert,y=geneID[,1:2],by.x="geneID",by.y="V2",all.x=TRUE) @@ -21,4 +24,4 @@ convert <- unique(convert) output <- merge(x=convert,y=countTable,by.x="GeneID",by.y="Geneid",all.x=TRUE) -write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE) \ No newline at end of file +write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)