[BioC] read counts in sliding windows
jasonlu68 at gmail.com
Wed Aug 3 04:46:39 CEST 2011
I would like to seek your advice with this.
Here I have a GRangesList and a GappedAlignments objects (an alignment
to the genome). For each GRanges (with length 1) in the GRangesList, I
would like to do a sliding window on its ranges and count reads from
each window. So far I wasn't able to find an efficient way to do this.
My problem is similar to this one:
But looping over the GRangesList (and using countOverlaps inside the
loop) takes significant time.
Thanks for any suggestions.
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