[BioC] distances for IRanges

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Tue Jun 8 17:51:51 CEST 2010

Assuming I have two IRanges, each with multiple ranges, like
  ir1 = IRanges(start = 3:6, width = 2)
  ir2 = IRanges(start = 10:17, width = 2)

Is there a fast way to compute a pairwise distance matrix between the
two sets, by which I mean
  ii = 1
  jj = 2
  width(gaps(c(ir1[ii], ir2[jj])))
where ii, jj would index into a result matrix.  Essentially this would
be an expanded version of findOverlaps, since any two ranges with
distance = 0, have an overlap.

Is such functionality available in IRanges, in an efficient
implementation (think of the case where the two IRanges have - say -
10,000 ranges or more)?


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