Hi, I have two GenomicRanges lists. I was wondering if there is any way to subtract the ranges of one element from the ranges in another element exactly like bedtools subtract (http://bedtools.readthedocs.org/en/latest/content/tools/subtract.html)? Thanks

For the two illustrated variations,

A = GRanges("A", IRanges(c(100, 200, 300), c(180, 220, 500)))
B = GRanges("A", IRanges(c(110, 320, 400), c(130, 350, 460)))

we have

> setdiff(A, B)
GRanges object with 6 ranges and 0 metadata columns:
      seqnames     ranges strand
         <Rle>  <IRanges>  <Rle>
  [1]        A [100, 109]      *
  [2]        A [131, 180]      *
  [3]        A [200, 220]      *
  [4]        A [300, 319]      *
  [5]        A [351, 399]      *
  [6]        A [461, 500]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

Or the -A option

> A[!A %over% B]
GRanges object with 1 range and 0 metadata columns:
      seqnames     ranges strand
         <Rle>  <IRanges>  <Rle>
  [1]        A [200, 220]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

These are for GRanges; if you have a GRangesList then it might help to show an example of the structures you're working with; psetdiff() might also be relevant.