[R] [BioC] comparing two tables

[Steve Lianoglou]

Hi,

On Wed, Oct 26, 2011 at 8:17 AM, Assa Yeroslaviz <frymor at gmail.com> wrote:
> Hi David,
>
> your function works just fine if I take nly the region into account. But
> unfortunately it does not consider the first column of the chromosomes.
> There can be an overlap between the two tables only if the regions are on
> the same chromosome. This is why the first column of both tables is a
> prerequisite for the analysis.
>
> I treid somehow to create a second argument to consider this, but until now
> without success.

Well, bioconductor has packages to deal with this type of data, and
these type of queries (overlaps) very efficiently.

Martin Morgan had sent you an email earlier explaining how you can use
the GenomicRanges packages to get what you're after ... I (highly)
suggest you go that route.

HTH,

-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