[BioC] stranded findOverlaps

[Robert Castelo]

dear list, and particularly, the IRanges developers,

i'm using the function findOverlaps from the IRanges package because i
need to find what stranded genomic intervals from one set (as a
RangedData object) overlap with what stranded genomic intervals from
another set (as another RangedData object). the problem is that i don't
what to consider overlaps between genomic intervals from different
strands.

i've been looking to the help page of findOverlaps (devel version, see
my sessionInfo() below) and searched through the BioC mailinglist and my
preliminary conclusion is that such an operation is not yet supported.

i've been thinking of using rdapply to break down the RangedData objects
into spaces and then again by the two strands but the problem is that
the query and subject indexes resulting of findOverlaps will not match
the dimension of the original RangedData objects.

so, i'd like to suggest that some option is added to this useful
function to restrict the overlapping search by strand. of course, if
this is somehow already implemented and i just missed it, then i'll be
very grateful if you let me know what function/parameter i should be
using.


thanks a lot!!
robert.

sessionInfo() 
R version 2.11.0 Under development (unstable) (2009-10-06 r49948) 
x86_64-unknown-linux-gnu 

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods
base     

other attached packages:
[1] IRanges_1.5.16