Merge branch 'remove.tpm.col' into 'develop'

Remove.tpm.col

Closes #67

See merge request !40

CHANGELOG.md

@@ -3,8 +3,11 @@
 * Output:
   * inputBag
   * outputBag
+* Remove gene details from tpm table
+* Add EntrezID translation to tpm table (from version specific reference)
 
 **Background**
+* Add GeneSymbol/EnsemblID/EntrezID translation files to references
 
 *Known Bugs*
 * outputBag does not contain fetch for processed data

workflow/scripts/convertGeneSymbols.R

@@ -19,6 +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$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
+write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
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