Fast way to find which gene a snp located.
3
0
Entering edit mode
@fabrice-tourre-4394
Last seen 9.5 years ago
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. Thank you very much.
SNP GenomicFeatures SNP GenomicFeatures • 3.4k views
ADD COMMENT
0
Entering edit mode
@michael-lawrence-3846
Last seen 2.2 years ago
United States
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. > 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]]
ADD COMMENT
0
Entering edit mode
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]]
ADD REPLY
0
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 4 months ago
United States
Fabrice, You could try annotatePeakInBatch (output = "overlapping", maxgap=0, multiple=TRUE) in ChIPpeakAnno package. Best regards, Julie On 5/5/11 8:00 AM, "Fabrice Tourre" <fabrice.ciup at="" 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. > > Thank you very much. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENT
0
Entering edit mode
hind ▴ 10
@hind-4643
Last seen 9.5 years ago
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?
ADD COMMENT
0
Entering edit mode
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]]
ADD REPLY

Login before adding your answer.

Traffic: 408 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6