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Question: how much positions overlapped for each pair of the pairs obtained by findoverlap.
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gravatar for vinod.acear
2.1 years ago by
vinod.acear20
India
vinod.acear20 wrote:

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.

ADD COMMENTlink modified 2.1 years ago by Hervé Pagès ♦♦ 13k • written 2.1 years ago by vinod.acear20
3
gravatar for Hervé Pagès
2.1 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

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.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Hervé Pagès ♦♦ 13k

Thanks herve

ADD REPLYlink written 2.1 years ago by vinod.acear20
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