Question: How to filter a list of SNPs?
0
8.4 years ago by
SimonNoël450
SimonNoël450 wrote:
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? Simon No??l CdeC
brain • 711 views
modified 8.4 years ago by Steve Lianoglou12k • written 8.4 years ago by SimonNoël450
Answer: How to filter a list of SNPs?
0
8.4 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, 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 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
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 No?l CdeC ________________________________________ De : Steve Lianoglou [mailinglist.honeypot at gmail.com] Date d'envoi : 13 mai 2011 17:10 ? : Simon No?l Cc : bioconductor at stat.math.ethz.ch Objet : Re: [BioC] How to filter a list of SNPs? Hi, 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 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