To be a little more helpful, you could do this:

rangesList <- tseqapply(ranges(from), seqnames(from), IntervalTree)

Then overlap queries will be fast, one chromosome at a time.

Michael

On Tue, Aug 3, 2010 at 6:45 PM, Michael Lawrence <michafla@gene.com> wrote:

> 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 <
> mailinglist.honeypot@gmail.com> 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>
>>
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>>
>
>

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