On Fri, Oct 1, 2010 at 6:58 AM, Kasper Daniel Hansen < [email protected]> wrote:
> Seems like the required changes hasn't yet been pushed from svn to the > builds. > > I do have one possible caveat: it is not clear to me how this would > work when the GRanges is not sorted by chromosome as I get > > > gr1 > GRanges with 3 ranges and 0 elementMetadata values > seqnames ranges strand | > <Rle> <IRanges> <Rle> | > [1] chr1 [1, 3] * | > [2] chr2 [2, 4] * | > [3] chr1 [6, 8] * | > > seqlengths > chr1 chr2 > NA NA > > as(gr1, "RangesList") > CompressedIRangesList of length 2 > $chr1 > IRanges of length 2 > start end width > [1] 1 3 3 > [2] 6 8 3 > > $chr2 > IRanges of length 1 > start end width > [1] 2 4 3 > > When I go back to the original GRanges I will need to interweave the > results from the RangesList. > > Yes, that's one issue. Easiest to just sort the GRanges up-front. Btw, RangedData can store things in interval trees without a separate object. > Of course, being able to do IntervalTrees directly on GRanges will > also be very convenient. > I agree. But that would take some work, since IntervalTrees have no notion of chromosome. Kasper > > > On Fri, Oct 1, 2010 at 12:05 AM, Michael Lawrence > <[email protected]> wrote: > > One easy way to get something like this: > > > > rangesList <- seqapply(as(gr, "RangesList"), IntervalTree) > > > > Then you'll have a RangesList of IntervalTree objects for range queries. > > > > Might need latest IRanges svn for this to work reliably (problem with > > subsetting IRanges with metadata). > > > > On Thu, Sep 30, 2010 at 6:48 PM, Kasper Daniel Hansen > > <[email protected]> wrote: > >> > >> I would like to see 'IntervalTrees for GRanges'. Specifically, if I > >> am repeatedly doing findOverlaps lookups on a big GRanges, I want to > >> be able to store the IntervalTrees that (right now?) gets computed > >> each time. > >> > >> This may of course already exist, in which case I would be satisfied > >> with a pointer :) > >> > >> Thanks, > >> Kasper > >> > >> _______________________________________________ > >> 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
