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

[Dario Strbenac]

Good day,

Thank you for these two suggestions. I have questions about both options.

GPos seems to have a limit on the number of bases it can represent. I get an error: Error in GPos(samplingAreas) : too many genomic positions in 'pos_runs'. What exactly is this limit ? Could it be added to the documentation ? I used all of the human chromosomes. There is also no documentation of the sample function for GPos objects.

Could regioneR be improved to consider strand ? It generates regions with no strand. I would like the regions to have a strand, since I have a strand-specific sequencing dataset, and for regions to be possibly chosen on the opposite strand to a masked region, such as when the genome is masked by transcripts for the purpose of choosing intergenic sequences.

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Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia