Hello

 

I am trying to conduct a sliding window analysis on a GRanges object. My
ranges are a list of 60272 single nucleotide positions representing high
confidence SNPs stored as IRanges object. I would like to retrieve the
list of GRanges row IDs for each  500bp window in the genome
(overlapping windows).

 

All the documentation I could find on sliding window functions such as
runsum, runmean, etc are all for Rle objects. 

 

Any idea where to start from? I can't figure out a way to pick windows
in the IRanges object across intervals, since each interval is
represented by a start and end position (same genomic position since
it's a single nucleotide long).

 

Any help will be greatly appreciated.

 

Thanks

 

-          Stefano




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