[BioC] Get Gene Information

[Vincent Carey]

the question is not very well-posed, but you can do something along
these lines with biomaRt

mart = useMart("snp")
ds = useMart("snp", data="hsapiens_snp")
allatt = listAttributes(ds)[,1]
allfilt = listFilters(ds)[,1]
getBM(allatt[c(1:5,9,59,60)], filters="refsnp", values="rs206116", mart=ds)

indeed the question of what 'association' between SNP and gene is of
concern needs to be made much clearer.  if you are interested in the
eQTL concept, the GGtools package has relevant tools and example data.


On Thu, Dec 17, 2009 at 9:27 AM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> 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
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