Hi

I am using tximport to generate the count matrix for RNA seq data:

txi <- tximport(files, type="salmon", tx2gene=tx2gene, ignoreTxVersion=TRUE,dropInfReps=TRUE)

I am using following to generate tx2gene

library(EnsDb.Mmusculus.v79)

txdf <- transcripts(EnsDb.Mmusculus.v79, return.type="DataFrame")

tx2gene <- as.data.frame(txdf[,c("tx_id", "gene_id")])

Is there a way so that I can get gene name instead of gene ids.

Regards

Tanya

> txdf <- transcripts(EnsDb.Mmusculus.v79, return.type = "DataFrame")
> txdf$symbol <- mapIds(EnsDb.Mmusculus.v79, txdf$gene_id, "GENENAME", "GENEID")
> tx2gene <- as.data.frame(txdf[,c("tx_id","symbol")])
> head(tx2gene)
               tx_id  symbol
1 ENSMUST00000082387   mt-Tf
2 ENSMUST00000179436    Cd99
3 ENSMUST00000082388 mt-Rnr1
4 ENSMUST00000177695  Ccl21c
5 ENSMUST00000082389   mt-Tv
6 ENSMUST00000082390 mt-Rnr2