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

RangesA and RangesB are clearly BED syntax, this can be done outside R in the command line with BEDtools, extremely fast and flexible with a dozen other options to work with genomic intervals. Then put the results back again into R.

https://code.google.com/p/bedtools/