[BioC] retrieve the gene symbols, full names etc given list of Entrez Gene IDs

Sean Davis sdavis2 at mail.nih.gov
Mon Jul 3 01:06:08 CEST 2006

Luo Weijun wrote:
> Hello all,
> Is there anyway to retrieve the gene symbols, full
> names (discription), or other gene information, given
> a list of Entrez Gene IDs (or the LocusLink) in
> Bioconductor. Obviously, one way is to query Entrez
> Gene web service ID by ID, but is there any way to get
> connected to that web service from within
> R/Bioconductor and retrieve the specific fields only(
> like gene symbol, Name, Chromosome, MIM etc) of Entrez
> Gene Records?
> biomaRt seems to require interactive R, and mine is
> command-line, and also it doesn't make one-on-one
> mapping table since multiple ensemble IDs map to one
> Entrez Gene ID, which is very annoying in making a
> good-looking annotation table.

You might want to look at the humanLLMappings package in the metadata 
section of bioconductor.  If I recall, this package is keyed using 
Entrez Gene IDs.  You will probably want to look at the mget() function 
for extracting information.  The annotate vignette also has some 
information that is relevant.


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