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
