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