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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.
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.
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Thanks herve