[BioC] can not link the genomic positions queried and their specific annotation, when getting genomic variants annotated by biomaRt package

[Steve Lianoglou]

Hi Mao,

Please include the bioc mailing list in the cc that you get the best
help possible.

On Tue, Feb 8, 2011 at 1:10 PM, Mao Jianfeng <jianfeng.mao at gmail.com> wrote:
> No.
>
> All your code just return several lines of various attributes (like
> defined in biomart), but it is none sense for me. I need my SNPs and
> various attributes they correspond to.
>
> I do not know if biomaRt can do that.
>
> Please read the simple example followed:
>
> I have SNPs like this:
> # SNPs,chr,start,end
> SNP_1,1,43,43
> SNP_2,2,56,56
>
> I would want to have annotations like this:
> ############################################
> #the chr, start, end here are for my SNPs not for the gos.
> ############################################
> # SNPs,chr,start,end,go_term
> SNP_1,1,43,43,go_1
> SNP_1,1,43,43,go_3
> SNP_2,2,56,56,go_100
> SNP_2,2,56,56,go_1000
>
> Not, just
> # chr,start,end,go_term
> 1,43,43,go_1
> 1,43,43,go_3
> 2,56,56,go_100
> 2,56,56,go_1000

So ... is the problem that the code I gave you previously gives you
"gene-level" annotations, and you want to reassociate them to snps, or
what?

Search the bioconductor archives for "snp annotation" and you'll find
a few things:

http://thread.gmane.org/gmane.science.biology.informatics.conductor/32759/focus=32846

And this might help too:

http://thread.gmane.org/gmane.science.biology.informatics.conductor/32267

If your problem is what I understand it to be, those threads may give
you a hint as to how you can use some tools in bioconductor to solve
your situation, even though they aren't answers to your *direct*
question.

Hope that helps,

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact