Hi,

I have two sets of Genomic Ranges which I'm intersecting using the findOverlaps of the GenomicRanges package:

df1 <- data.frame(chr=rep("chr1",6), start=c(10033259,10060726,98674166,10067579,10067607,11169988), end=c(10033289,10060783,98674223,10067654,10067664,11170044), strand=c("-","-","+","+","+","+"))

df2 <- data.frame(chr=rep("chr1",3),start=c(10024601,10033258,10033258),end=c(10038168,10033323,10033323),strand=c("-","-","-"))

df1.gr <- makeGRangesFromDataFrame(df1,seqnames.field="chr",start.field="start",end.field="end",strand.field="strand")

df2.gr <- makeGRangesFromDataFrame(df2,seqnames.field="chr",start.field="start",end.field="end",strand.field="strand") dfs.ol <- findOverlapsdf1.gr,df2.gr)

My question is how to extract the actual overlapping coordinates of each of the hits in the returned value of findOverlaps (dfs.ol)?

I know that the intersect function returns the collapsed intervals in the query genomic ranges which intersect with a search genomic ranges. But what I really need for each overlap between gr1 and gr2 are the coordinates of the overlap, in addition to the indices of the genomic ranges which overlap (in the returned Hits object).

You can use pintersect:

overlaps.gr <- pintersect(df1.gr[queryHits(dfs.ol)], df2.gr[subjectHits(dfs.ol)])

If you want all the results in one object, you can add the indices as metadata columns:

overlaps.gr$df1_hit <- queryHits(dfs.ol)
overlaps.gr$df2_hit <- subjectHits(dfs.ol)