Great! I was able to use annotatePeakInBatch as per Julie's recommendation to get what I was looking for. Thanks for the help! On Tue, Feb 26, 2013 at 9:10 AM, Adaikalavan Ramasamy < adaikalavan.ramasamy@gmail.com> wrote: > I asked a similar question last week and got the solution with the help of > Valerie. I was looking for flanking genes and not necessarily the closest. > If you are interested, see my blog at > http://adairama.wordpress.com/2013/02/15/functionally-annotate-snps- and-indels-in-bioconductor/ > > Regards, Adai > > > On Tue, Feb 26, 2013 at 1:21 PM, Zhu, Lihua (Julie) < > Julie.Zhu@umassmed.edu> wrote: > >> Molly, >> >> You might want to try annotatePeakInBatch in ChIPpeakAnno package with >> parameter output="both". >> >> Best regards, >> >> Julie >> >> >> On 2/25/13 4:35 PM, "Molly Hanlon" <hanlonmt@gmail.com> wrote: >> >> > Hi list, >> > >> > I've been using R for some time, but am new to bioconductor/biomaRt. >> Please >> > pardon that. >> > >> > I have a list of a couple thousand SNPs and I'm looking for the closest >> > gene to each of them. Looking just within the gene, I only get a result >> > for about a third of them, so I obviously need something a bit more >> robust. >> > Searching the archives, I've found mention of the findClosestGene in >> ACME, >> > however, I work in rice, so this isn't much help. Ideally, I'd like to >> > enter a position, say "9:12344567" and get an output that it lies 1234 >> bp >> > upstream from Loc_OsXXXXXX. >> > >> > I've also seen suggestions that include getting a data frame of all the >> > gene positions and then using findOverlap with my frame, though I'm not >> > sure this would work because I have no strand information for my query >> and >> > they're single base pairs, thus without a range. >> > >> > Feel free to correct my assumptions, but any additional help you can >> > provide would be wonderful. >> > >> > Many thanks, >> > Molly >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 >> >> _______________________________________________ >> 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]]