Answer: How to filter a list of SNPs?
2011/5/13 Simon No?l <simon.noel.2 at="" ulaval.ca="">:
> ? Hello every one. ?I have a really big list of SNPs from all the
> ? I want to restrict that llist to SNPs that point to gene expressed
> ? 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
(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 "*")
(5) shorter.snp.list <- subsetByOverlaps(snps,
Graduate Student: Computational Systems Biology
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