Commit 7e35e638 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Merge branch 'develop' into 'master'

Develop

See merge request !41
parents eedb6628 64c587de
Pipeline #7981 passed with stages
in 96 minutes and 33 seconds
......@@ -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
......
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......@@ -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$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
\ No newline at end of file
write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
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