ccing Halian On 05/01/2012 08:20 AM, Valerie Obenchain wrote: > Hi Halian, > > gr1 <- GRanges(seqnames = "chr2", ranges = IRanges(3, 6)) > gr2 <- GRanges(seqnames = c("chr1", "chr1"), ranges = > IRanges(c(7,13), width = 3)) > gr3 <- GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(c(1, > 4), c(3, 9))) > grl <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3) > > grl[seqnames(grl) == "chr2"] > > Valerie > > > On 05/01/2012 07:26 AM, Halian Vilela wrote: >> Hey guys, >> >> I would like to know if there are any methods of efficiently subset a >> GRangeList by it seqnames. >> >> I have something like this: >> >> >> GRangesList of length 86046: >> $1 >> GRanges with 27 ranges and 3 elementMetadata values: >> seqnames ranges strand | exon_id >> exon_name exon_rank >> <rle> <iranges> <rle> |<integer> <character> <integer> >> [1] chr1 [66999065, 66999090] + | >> 1<na> 1 >> [2] chr1 [66999928, 67000051] + | >> 2<na> 2 >> [3] chr1 [67091529, 67091593] + | >> 3<na> 3 >> [4] chr1 [67098752, 67098777] + | >> 4<na> 4 >> [5] chr1 [67099762, 67099846] + | >> 5<na> 5 >> [6] chr1 [67105459, 67105516] + | >> 6<na> 6 >> [7] chr1 [67108492, 67108547] + | >> 7<na> 7 >> [8] chr1 [67109226, 67109402] + | >> 8<na> 8 >> [9] chr1 [67126195, 67126207] + | >> 9<na> 9 >> ... ... ... ... ... ... >> ... ... >> >> >> >> In which each element ($1,$2,$3,...) represents a transcript and it >> set of exons... >> >> In the seqnames colum I have the chromosomes ranging from 1 to Y (all >> 24 human cromosomes), what I would like to know is how to get just the >> elements accounting for chromosome 14... >> >> I have made successfully by unlisting the structure into a huge normal >> GRange and then subseting normally: >> >> ex<- unlist(ex_tx) >> ex14<- ex[which(seqnames(ex) == "chr14")] >> >> >> But obviously I lose the GRangesList structure. So are there any way >> to subset this directly in the GRangesList without the need to unlist, >> in a way that my result is also a GRangesList ? >> >> Thanks, >> Halian >> >> [[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 >