I was inspired by this to add an experimental (just for fun) "by" argument to sort,GenomicRanges that supports sorting by a formula in the environment of the GRanges. So now you can do: sort(CBGIs, by=~ID+start) Just an experiment; feel free to get rid of it. On Thu, Feb 13, 2014 at 10:14 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 02/13/2014 07:02 AM, d r wrote: > >> Hi there >> >> I am looking for a way to reorder a GRanges object using its metadata. >> Here is a sample of my GRanges object: >> >> GRanges with 1122060 ranges and 4 metadata columns: >> seqnames ranges strand | >> ID TSS >> <rle> <iranges> <rle> | >> <character> <integer> >> [1] chr1 [66993729, 66993928] + | >> chr1:66998729-66999824 chr1:66999824-66999824 + 1 >> [2] chr1 [66993929, 66994128] + | >> chr1:66998729-66999824 chr1:66999824-66999824 + 1 >> [3] chr1 [66994129, 66994328] + | >> chr1:66998729-66999824 chr1:66999824-66999824 + 1 >> [4] chr1 [66994329, 66994528] + | >> chr1:66998729-66999824 chr1:66999824-66999824 + 1 >> [5] chr1 [66994529, 66994728] + | >> chr1:66998729-66999824 chr1:66999824-66999824 + 1 >> ... ... ... ... ... >> ... ... >> [1122056] chr22 [51226318, 51226517] + | >> chr22:51221773-51222156 chr22:51222156-51222156 + 29143 >> [1122057] chr22 [51226518, 51226717] + | >> chr22:51221773-51222156 chr22:51222156-51222156 + 29143 >> [1122058] chr22 [51226718, 51226917] + | >> chr22:51221773-51222156 chr22:51222156-51222156 + 29143 >> [1122059] chr22 [51226918, 51227117] + | >> chr22:51221773-51222156 chr22:51222156-51222156 + 29143 >> [1122060] chr22 [51227118, 51227317] + | >> chr22:51221773-51222156 chr22:51222156-51222156 + 29143 >> >> I want to order it so the ranges will be sorted first by the ID >> metadata,then by start (ranges with the same value for this metadata >> are all subsets of a larger range, so they are on the same >> chromosome). >> >> I have implemented that coercing the GRanges into a data frame, >> ordering its row and then coercing back to GRanges: >> >> grdf<-as.data.frame(CPGIs) >> grdf<-grdf[order(grdf$ID,grdf$start),] >> CPGIs<-GRanges(seqnames=grdf$seqnames, ranges=IRanges(grdf$start, >> grdf$end),strand=grdf$strand, ID=grdf$ID, TSS=grdf$TSS, >> HGNC_symbol=grdf$HGNC_symbol, refseq_symbol=grdf$refseq_symbol) >> > > I think you're looking for > > o = order(CPGIs$ID, start(CBGIs)) > CBGIs[o] > > ? > > Martin > > > >> >> Which works, but is somewhat cumbersome. Is there a way to reorder the >> Granges object without resorting to a data frame? >> >> Thanks in advance >> >> Dolev Rahat >> >> [[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 >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > > _______________________________________________ > 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]]