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Old 01-11-2016, 10:16 AM   #1
jurat
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Location: Italy

Join Date: Jan 2016
Posts: 1
Post How to iterate GRanges objects in R for parallel processing more than one bed files?

Hi:
part of my job is to process bunch of bed files in parallel by using R. I have read each bed files as GRanges objects in R. I used GenomicRanges::findOverlaps(query, subjects) to observe overlapped peak regions. How can I efficiently iterate over each GRanges objects one by one with respect set of GRanges objects from second bed files.

Here is my example to show genome interval:

Code:
GRanges object with 6 ranges and 2 metadata columns:
      seqnames           ranges strand |        name     score
         <Rle>        <IRanges>  <Rle> | <character> <numeric>
  [1]     chr1 [ 32727,  32817]      * | MACS_peak_1      8.69
  [2]     chr1 [ 52489,  52552]      * | MACS_peak_2      4.26
  [3]     chr1 [ 65527,  65590]      * | MACS_peak_3      4.19
  [4]     chr1 [ 65773,  65904]      * | MACS_peak_4      2.02
  [5]     chr1 [ 66001,  66117]      * | MACS_peak_5      5.66
  [6]     chr1 [115700, 115769]      * | MACS_peak_6     10.30
overlap<- findOverlaps(bed.1[1], bed.2) # needs to update all GRanges object of bed.1;

How can I do that ? Please help me out !!!
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