To be a little more helpful, you could do this: rangesList <- tseqapply(ranges(from), seqnames(from), IntervalTree)
Then overlap queries will be fast, one chromosome at a time. Michael On Tue, Aug 3, 2010 at 6:45 PM, Michael Lawrence <[email protected]> wrote: > The problem is that IntervalTree will not respect the separation of > spaces/chromosomes. Any time you call ranges() on a GRanges, you lose that > information. > > Michael > > > On Tue, Aug 3, 2010 at 6:22 PM, Steve Lianoglou < > [email protected]> wrote: > >> Hi, >> >> I find it might be a bit more convenient to create an >> as(GRanges.object, "IntervalTree") method, so one doesn't have to >> check if the ranges object is an IRanges or GRanges object. Would you >> agree? >> >> For various reasons, I pass these types of objects into similar >> places, so (IMHO) adding a setAs method in the GenomicRanges would be >> helpful: >> >> setAs("GRanges", "IntervalTree", function(from) as(ranges(from), >> "IntervalTree")) >> >> Cheers, >> -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<http://cbio.mskcc.org/%7Elianos/contact> >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
