I have got overlapping pairs list using findoverlap function on two granges, i want to know  how much positions overlapped for each  pair of  the pairs obtained by findoverlap.

Hi,

So you have a Hits object that you got by calling findOverlaps() on your GRanges objects query and subject, e.g. by doing something like:

hits <- findOverlaps(query, subject, ...)

Now you can get the corresponding overlap as a range for each pair in hits with:

overlap <- pintersect(query[queryHits(hits)],
                      subject[subjectHits(hits)])

and the number of positions in each overlap with:

width(overlap)

Cheers,

H.