Develop

workflow/scripts/convertGeneSymbols.R

@@ -10,9 +10,6 @@ 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=Entrez,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)
@@ -22,6 +19,6 @@ convert <- convert[,-1]
 colnames(convert) <- c("GeneID","EntrezID")
 convert <- unique(convert)
 
-output <- merge(x=convert,y=countTable,by.x="GeneID",by.y="Geneid",all.x=TRUE)
+output <- merge(x=convert,y=countTable[,c("Geneid","count","tpm")],by.x="GeneID",by.y="Geneid",all.x=TRUE)
 
 write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)