On Fri, May 6, 2011 at 2:54 PM, Arnaud Amzallag
<arnaud.amzallag@gmail.com>wrote:

> Dear IRanges developers,
>
> runsum is a very fast and convenient function to compute on Rle coverages,
> for instance. However when it is run on several chromosomes and several
> samples, it can get very memory intensive. For instance on human chromosome
> 1, it outputs a vector of length 250 millions, so for several full genomes
> it is quickly billions of numbers in memory.
>
>
I would have expected the result to be an Rle, which would be fairly memory
efficient.


> However, often you don't need a single base resolution. I wanted to
> suggest, if it is possible, to add a parameter by which one could have the
> sliding window to slide by a user defined step, rather than always "step=1",
> as it is now. Such that runsum(myRle, k=1e4, step = 1000) would return the
> equivalent of a wig file, for each 10 kilobases of the genome, without
> saturating the memory of the server.
>
> I tried with sum(Views(myRle, ir)), it is less memory intensive but it is
> much slower. So that amelioration would give the best of both worlds, fast
> and memory efficient.
>
>
Have you tried viewSums(Views(myRle, ir))?


> kind regards,
>
> Arnaud Amzallag
> Research Fellow
> Mass general Cancer Center / Harvard Medical school
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