[BioC] RE : How to filter a list of SNPs?

[Simon Noël]

I can modify the question...

 Where can I find a complete list of all gene expressed in the brain...  From that, I have a good idea of what to do.

Simon Noël
CdeC
________________________________________
De : Steve Lianoglou [mailinglist.honeypot at gmail.com]
Date d'envoi : 13 mai 2011 17:10
À : Simon Noël
Cc : bioconductor at stat.math.ethz.ch
Objet : Re: [BioC] How to filter a list of SNPs?

Hi,

2011/5/13 Simon Noël <simon.noel.2 at ulaval.ca>:
>
>   Hello every one.  I have a really big list of SNPs from all the genome and
>   I want to restrict that llist to SNPs that point to gene expressed in the
>   brain.  How should I procede and with wich package?

To help you get better answers, can you explain what you mean by a SNP
"point[ing] to" an expressed gene?

Here's an answer to a question you *might* be asking:

If you are talking about filtering your SNP list to the SNPs that are
in cis to genes that are expressed, I would:

(1) Get the appropriate gene expression data so you can get a list of
expressed genes
(2) Use GenomicFeatures to build a TranscriptDb using your gene
annotations of your choice
(3) extend the transcripts from (2) by some (cis) distance you
determine is appropriate and store in `extended.expressed.genes`
(4) store your SNPs as a GRanges object (I guess set strand to "*") named `snps`
(5) shorter.snp.list <- subsetByOverlaps(snps, extended.expressed.genes)
(6) ...
(7) publish

--
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