I want to get coordinates of human genes from my list (consisting of hgnc genes id) using GenomicFeatures and TxDb.Hsapiens.UCSC.hg19.knownGene R packages from Bioconductor.


my_genes = c("INO80","NASP","INO80D","SMARCA1")

select(txdb, keys = my_genes,

However, it doesn't' work because txdb doesn't take hgnc identifiers; how can it be solved? I couldn't find any appropriate keytype that will support hgnc and not sure how to match hgnc id I have and GENEID from txdb.


1 Answer 1


Answer from @devon-ryan, converted from comment:

Try a UCSC gene ID instead. For those genes they'd be: uc001zni.3 (INO80), uc002vaz.4 (INO80D), uc004eup.4 or uc004eun.4 (SMARCA1) and uc001coj.2, uc010olq.2, uc010olr.2, uc001coi.2 or uc001col.2 (NASP). You might have to omit the versions (the .4 part, for example).


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.