[BioC] Gene symbol update.
Marc Carlson
mcarlson at fhcrc.org
Sat Mar 16 01:32:32 CET 2013
Hi Jinyan,
It depends. It depends on what you are using for annotations, and also
which version of bioconductor/R you are using. If you are using
packages from the release last fall for example, then those things will
have been updated back then. We are currently in the middle of updating
these things right now for the upcoming spring release. And if you are
using a web service like biomaRt, things may have already been updated
very recently. So it depends on what you are using for annotations...
Unless maybe you are actually asking about what to do with a list of old
gene symbols that you simply want to modernize. In that case, I think
you want do do something like this:
library(org.Hs.eg.db)
select(org.Hs.eg.db, keys = c("CRSP6","KIAA0804"), cols="SYMBOL",
keytype="ALIAS")
Hope this helps,
Marc
On 03/14/2013 10:09 PM, Jinyan Huang wrote:
> Dear expert,
>
> Is there some bioconductor package to update Gene symbol ?
>
> e.g.
> CRSP6 update to MED17.
> http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/gene/9440
>
> KIAA0804 update to VPS8
> http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/gene/?term=KIAA0804
>
> --
> Best wishes,
>
> Jinyan HUANG
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor
mailing list