[Bioc-sig-seq] GenomicRanges wishlist: IntervalTrees for GRanges

[Ivan Gregoretti]

This sounds like a serious increase in computing efficiency.

Can somebody update the pertinent documentation to include an example
using this strategy?

Thank you,

Ivan



On Fri, Oct 1, 2010 at 12:05 AM, Michael Lawrence
<lawrence.michael at gene.com> 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 <
> kasperdanielhansen at gmail.com> 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
>>
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