[BioC] Gene-snp matching

[Bucher Elmar]

Hi Mohamed, 

I never had to link snips to genes. But I checked the documentation of
the biomaRt bioconductor package.

http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html
 
This package enables you to use ensembl mart in R. 
http://www.ensembl.org/index.html
http://www.ensembl.org/biomart/martview/

I checked there the attributes and filters for the Homo Sapiens. Several
snp related attributes and filters are to find. So I think this package
will be able to solve your problem.   

 
If you work at Homo Sapiens the package SNPlocs.Hsapiens.dbSNP.20090506,
which I found in addition on the bioconductor homepage, might as well be
useful.

http://www.bioconductor.org/packages/release/data/annotation/html/SNPloc
s.Hsapiens.dbSNP.20090506.html

But if the biomaRt packge works, then myself would prefer the biomaRt...
but that's just a matter of taste and you maybe better listen to a
person who works a lot whit snp data, if one of those gives you answer.

Anyhow, hope this help get you at least started. 

So long, Elmar 



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Message: 2
Date: Mon, 14 Sep 2009 11:32:38 +0200
From: Mohamed Lajnef <Mohamed.lajnef at inserm.fr>
Subject: [BioC] Gene-snp matching
To: bioconductor at stat.math.ethz.ch, Sean Davis <seandavi at gmail.com>
Message-ID: <4AAE0DB6.9070606 at inserm.fr>
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Hi  All,

I have a list of genes and I want the snps matching of these genes (the 
other way too e.g: Snps ----> genes)

Is there any R package  to do this ?

Regards
M

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Mohamed Lajnef
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