[Bioc-devel] Strand-Awareness for Restrict Function

Dario Strbenac dstr7320 at uni.sydney.edu.au
Mon Feb 15 06:00:07 CET 2016


The restrict function currently has no strand settings. This would be useful if I am creating fixed size windows, 50 bases wide, by sampling the start positions of the windows from a GRanges object. I'd like to restrict the GRanges object being sampled from, but only on the - stand when removing positions 1 to 50 and only on the positive strand when removing positions within the last 50 bases of the chromosome. So, a strand-aware version would be useful, to avoid sampling start positions too close to the ends of chromosomes. I suppose that setdiff will be a suitable alternative, if the first and last 50 bases are calculated of each chromosome.

Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050

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