Finding overlap in ranges with R

Question

I have two data.frames each with three columns: chrom, start & stop, let\'s call them rangesA and rangesB. For each row of rangesA, I\'m looking to find which (if any)

Answer 1

This would be a lot easier / faster if you can merge the two objects first.

ranges <- merge(rangesA,rangesB,by="chrom",suffixes=c("A","B"))
ranges[with(ranges, startB <= startA & stopB >= stopA),]
#  chrom startA stopA startB stopB
#1     1    200   250    200   265
#2     5    100   105     99   106