[BioC] find overlap of bed files of different length

[Duke]

On 1/31/11 1:20 PM, Kasper Daniel Hansen wrote:
> Use findOverlaps to find all cases.  This is usually the hard and big
> computation.  Then use for example pintersect() to compute the actual
> overlap in percent.  There might be some tedious coding involved.

Thanks for your suggestion Kasper, though honestly I have not tried it 
yet. But based on what Martin and you suggested, I thought the final 
code will not run fast because of extracting to strand/subset and 
running each. Especially my task is a little more complicated: I need to 
find gene expressions (counting sequences in exonic regions of each 
gene). I also gave BEDTools a try, but it does not fulfil my needs 
(extremely slow for a gene list of 28k).

I ended up with coding a c++ code to do the job. Thanks for all of your 
suggestions and helps guys.

D.