[BioC] SNP to Gene mapping (GWAS)

[Paul Leo]

This works for me, will give you Vega 35

library(biomaRt)
listMarts(host="may2009.archive.ensembl.org",path="/biomart/martservice",archive=FALSE)
mart=useMart("ENSEMBL_MART_SNP",dataset="hsapiens_snp",
host="may2009.archive.ensembl.org",path="/biomart/martservice",archive=FALSE)
getBM(mart=mart, filters="refsnp", value="rs3094315",
       attr=c("chr_name", "chrom_start",
       "ensembl_gene_stable_id"))

your could could dump the parts of org.Hs that you want to a table and
keep that...


-----Original Message-----
From: Tim Smith <tim_smith_666 at yahoo.com>
To: Sean Davis <seandavi at gmail.com>
Cc: Vincent Carey <stvjc at channing.harvard.edu>, bioc
<bioconductor at stat.math.ethz.ch>
Subject: Re: [BioC] SNP to Gene mapping (GWAS)
Date: Sun, 25 Oct 2009 17:20:44 -0700 (PDT)

getBM(mart=mart49, filters="refsnp", value="rs3094315",
       attr=c("chr_name", "chrom_start",
       "ensembl_gene_stable_id"))