Hello, I have a GRanges object gr comprising all (human) chromosomes. And now I would like to retrieve all ranges of one special chromosome (e.g. Chromosome 11). I dont find a way neither with window, subset or seqselect. How does it work? Thanks Wim [[alternative HTML version deleted]]

Hi, On Wed, Jan 9, 2013 at 3:23 PM, Wim Kreinen <wkreinen at="" gmail.com=""> wrote: > Hello, > > I have a GRanges object gr comprising all (human) chromosomes. And now I > would like to retrieve all ranges of one special chromosome (e.g. > Chromosome 11). I dont find a way neither with window, subset or seqselect. > How does it work? Assuming your 11th chromosome is named "chr11": R> stuff <- gr[seqnames(gr) == 'chr11'] -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

Wim, If you show us how you created you GRanges, what it looks like, how exactly you've tried to " retrieve all ranges of one special chromosome", and what you expect the answer to be (i.e. as a GRanges), we will be well equipped to help. Cheers, ~Malcolm .-----Original Message----- .From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of Wim Kreinen .Sent: Wednesday, January 09, 2013 2:24 PM .To: bioconductor at r-project.org .Subject: [BioC] subset GRanges . .Hello, . .I have a GRanges object gr comprising all (human) chromosomes. And now I .would like to retrieve all ranges of one special chromosome (e.g. .Chromosome 11). I dont find a way neither with window, subset or seqselect. .How does it work? . .Thanks .Wim . . [[alternative HTML version deleted]] . ._______________________________________________ .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