Some ideas: - Turn the IntervalTree into a list/array of nodes that can be subset/reordered with shallow copying (just copy the pointers to the nodes), and the index would be secondary. The index in the array could be stored in each node, for lookup during overlap queries. Right now, as far as I can tell, GIntervalTree will get confused if the user reorders e.g. via [.
- Make IntervalTree aware of the sequence/chromosome, e.g., have a hash of trees, which is trivial since seqnames is already a factor. Michael On Wed, Apr 3, 2013 at 9:29 AM, Hector Corrada Bravo <hcorr...@gmail.com>wrote: > Yep, I didn't comment on that, but I agree that abstracting how > GRanges stores ranges would make this more elegant. Right now > ranges(GRanges) is specified to be of IRanges class instead of the > abstract Ranges class. > > If it were the latter then GIntervalTree can be a subclass of > GenomicRanges, in a similar way that IntervalTree is a subclass of > Ranges. > > On Wed, Apr 3, 2013 at 12:23 PM, Michael Lawrence > <lawrence.mich...@gene.com> wrote: > > 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
