On Thu, May 5, 2011 at 6:44 AM, Michael Lawrence <michafla@gene.com> wrote: > > > On Thu, May 5, 2011 at 5:00 AM, Fabrice Tourre <fabrice.ciup@gmail.com>wrote: > >> Dear list, >> >> I have 8,000 snps. Each snp it has chromosome and genome position >> information. I want to know which genes these snps located separately. >> Does anyone have suggestion how can I get this information? >> >> I think GenomicFeatures packages is hard to do this. >> >> > Actually, it's not so hard. > > Say you have a TranscriptDb object from e.g. makeTranscriptDbFromUCSC(), > then you can just get the transcripts: > > tx <- transcripts(txdb, columns = "gene_id") > > And match the SNPs to them: > > values(snps)$gene_id <- values(tx)$gene_id[match(snps, tx)] > > Your SNPs should be a GRanges, RangedData or RangesList. > > Correction: snps must be a GRanges the way I wrote that. For a RangedData, it would be: snps$gene_id <- values(tx)$gene_id[match(snps, tx)] > Thank you very much. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]

Hi. You'll need to be much more specific about your question in order to get good help. Please rephrase your question with more details about what you have done and what you want to accomplish. Sean On Wed, May 11, 2011 at 4:19 PM, hind <hind.bou@hotmail.com> wrote: > Hi, > > I need this program in order to localise SNPs but i don't know where I can > find > it and how it works , so can you help me please and give me some > instrcutions? > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]