Hi,

I have a GRanges object:

gr <- GRanges("chr1", IRanges(c(10000, 11000, 12050, 13000, 14500,20000,23000), width=100))

I want to get a list of sets of regions that fall within 2kb of one another, eg [1],[2],[3],[4],[5]. But not a 2kb tile, e.g. which could take in [1],[2], and [3],[4],[5] but cannot join them as one element of the list.

GRanges object with 7 ranges and 0 metadata columns:
      seqnames         ranges strand
         <Rle>      <IRanges>  <Rle>
  [1]     chr1 [10000, 10099]      *
  [2]     chr1 [11000, 11099]      *
  [3]     chr1 [12050, 12149]      *
  [4]     chr1 [13000, 13099]      *
  [5]     chr1 [14500, 14599]      *
  [6]     chr1 [20000, 20099]      *
  [7]     chr1 [23000, 23099]      *

Issue is with how to allow 2kb limit to 'reset' and hence 'resample' row [3],[4],[5] in my example. Hope that is clear, I looked at slidingWindow() but not clear if this can achieve that outcome? Essentially, I would like the sliding window to end when the last position is more than 2kb away from the next. I have a Perl script, but should be relatively easy in GRanges, or no? I have searched but unsure of how to term this function.

Kind regards,

Bruce.

Probably want something like:

bins <- reduce(x, min.gapwidth=2000L)

If you want to know which ranges fell into each bin, use , with.revmap=TRUE.