[BioC] IRanges: how to emulate findOverlaps(multiple=TRUE)?

[Steve Lianoglou]

Hi Michael,

On Sat, Apr 28, 2012 at 3:23 AM,  <Michael.Dondrup at uni.no> wrote:
> Hi,
> I have some R-scripts that rely on the argument multiple=TRUE
> in findOverlaps(). However, this option has been removed in the latest
> release it seems, as it was said to be deprecated before. But now
> our scripts don't work any more, and removing the parameter
> simply yields a different output format and is not an option.
>
> Is there a quick way to  bring the behavior of it back, with respect to
> output format and overlap matching?

I'm sure the folks at bioc-central will recall exactly how
multiple=TRUE does, but some of us have a harder time remembering the
ins/outs of the findOverlaps internals but would still like to try to
help ;-)

Could you maybe provide a small example (few ranges in the query, a
few in the subject) that would result in a findOverlaps() call w/
multiple overlaps and show us what you'd like to get out of it so that
your scripts can keep humming?

Thanks,
-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