Hi Hector, That's interesting, thanks for passing this along. I'm still wishing that somehow GRanges itself could abstract the way it stores ranges. I know that Herve/Patrick had some reasons for depending specifically on GRanges. One reason was probably convenience at the C level, but it wouldn't be hard to create a Ranges abstraction at the C level, as well.
Michael On Tue, Apr 2, 2013 at 5:40 PM, Hector Corrada Bravo <hcorr...@gmail.com>wrote: > Hello bioc-develers, > > I'm writing an application where lots findOverlap calls are made on > static GRanges objects. For IRanges we can create persistent > IntervalTree objects that would serve the multiple overlap query > use-case. There is no equivalent for GenomicRanges objects, so I'm > proposing an implementation for this. > > Please check > http://github.com/hcorrada/GenomicIntervalTree > > There's a first cut implementation there you can test by installing > this skeleton package. E.g, > > > library(devtools) > > install_github("GenomicIntervalTree", username="hcorrada", subdir="pkg") > > library(GenomicIntervalTree) > > Let me know what you think. > > Cheers, > Hector > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
