An esay but not optimised solution to get the N genes around will be to set a "big" range around the gene of interest and use the liste you get to take the N gene. It's not bad when N is small but it's not the best solution when N is big. Simon No?l CdeC ________________________________________ De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de Steve Lianoglou [mailinglist.honeypot at gmail.com] Date d'envoi : 21 juillet 2011 11:40 ? : James Perkins Cc : Bioconductor at r-project.org Objet : Re: [BioC] Find all the genes n genes either side on the chromosome Hi, On Thu, Jul 21, 2011 at 11:23 AM, James Perkins <jperkins at="" biochem.ucl.ac.uk=""> wrote: > Dear all, > > Given a gene of interest, is there an easy way to get the n nearest > genes either side (i.e. 5' and 3' direction) on the chromosome, > without leaving R? > > I looked in biomart for a way to get the nearest gene either side but > couldn't see anything obvious. If this exists I suppose that could be > one way, just repeat the getBM call n times. > > Any pointers at how to go about doing this would be very gladly received. Bird's eye view: Create yourself a TranscriptDb object and extract your genes of interest from it into a GRanges object (perhaps by calling `transcripts`) `precede` and `follow` will find you neighboring ranges to a query given a subject, which will give you the closes genes on either side of your points of interest. I'll leave getting N such genes as an exercise for the reader :-) -steve -- 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 _______________________________________________ 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