I have a matrix of gene counts which I'm going to use as input for DESeq. Right now, each gene is labeled by its Ensemble transcript ID, but I'd like to convert these to their HGNC symbols before I input them into DESeq for analysis. I'm attempting to do this conversion using biomaRt, however, this is my first time using the program, and I'm running into issues. Here is my current code:
library("biomaRt") mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl") transcript.ids <- rownames(txi.kallisto$counts) hgnc_symbols <- getBM(attributes = "hgnc_symbol", filters = "ensembl_transcript_id", values = transcript.ids, mart = mart)
Printing hgnc_symbols shows that it isn't what I want:
>ghnc_symbols  hgnc_symbol <0 rows> (or 0-length row.names)
Lastly, here is what the input transcript IDs look like:
> head(rownames(txi.kallisto$counts))  "ENSMUST00000178862.1" "ENSMUST00000178537.1" "ENSMUST00000196221.1"  "ENSMUST00000179664.1" "ENSMUST00000177564.1" "ENSMUST00000179520.1"