[Bioc-devel] Efficient Random Sampling of Positions in GRanges

Dario Strbenac dstr7320 at uni.sydney.edu.au
Tue Feb 16 12:00:11 CET 2016


There is no convenience function to sample nucleotide positions from a GRanges object. My approach is to generate a GRanges of every chromosomal position with a width of 1, then find the overlaps with the desired ranges (admissible regions), then sample the positions that overlapped. The construction of the GRanges object containing every chromosome position is inefficient, as is finding its overlaps with another GRanges object. Could an optimised function for this task be added to GenomicRanges ?

Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050

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