[BioC] Get Gene Information

[James W. MacDonald]

Hi Peter,

Peter Ganske wrote:
> Hello everybody, i got  a list of SNPs. Is there a package to get
> informations about the association with genes automatically? I want
> to check the SNPs and collect some informations about them. Would be
> amazing, if anybody can help me out. Thanks in advance Peter

Not that I know of. And certainly not something that you can plug in a 
bunch of rs numbers and automagically get all kinds of info returned.

Any response depends on what you mean by 'association with genes'. If 
you mean something naive like 'is this SNP between the 5' and 3' UTR of 
some gene, then you could use the org.Xx.eg.db package for your organism 
along with the IRanges package to find SNPs that are 'in' genes.

Anything more sophisticated than that will likely require you to write 
your own functions and/or use software outside the Bioconductor project.

Best,

Jim


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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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