Entering edit mode
1 day ago
Khôi
•
0
Hi everyone, I want to ask for ways I could do to convert mRNA ID into the gene ID. I'm using biomaRt package in R, and it works for most of the mRNA but not all of them:
ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
getBM(
attributes = c("refseq_mrna", "ensembl_transcript_id", "external_gene_name"),
filters = "refseq_mrna",
values = "NM_000347" (for example),
mart = ensembl
)
Yet, some of the mRNA transcripts can't be looked up this way. I want to ask how do I query those without refseq_mrna data? Thank you sm.
You can also use EntrezDirect like so
If you also want to get aliases for the gene
Hi, thank you for your suggestion! The command gave me this error:
I realized it was because I used a very obsolete version of entrez-direct. Upgraded it to 22.4 helps!