[Bioc-sig-seq] Cached GenomicRanges or RangedData Objects?

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Oct 11 17:50:44 CEST 2010

Hi Chuck,

On Mon, Oct 11, 2010 at 11:24 AM, Charles C. Berry <cberry at tajo.ucsd.edu> wrote:
> We are liking the idioms that go with GenomicRanges and RangedData Objects
> (follow, precede, findOverlaps, etc), but we are bumping up against memory
> demands of loading very large objects.
> Is there now or will there soon be a cached version of these that will
> lessen our memory requirements?
> If not, is there a cookbook as to how to create and save cached versions of
> these objects.
> Or maybe a place to look in the bioConductor codebase to get some ideas of
> how to go about constructing cached versions of these classes?

I'm not sure what you mean by caching -- do you want them serialized
to disk and you read off parts when you need them, or?

Also -- I typically split my data and processing to work on a
chromosome by chromosome basis -- even though the GenomicRanges
infrastructure allows you to keep ranges spanning multiple chromosomes
in one object. Although it's a bit more book keeping code on my part,
I find that doing so helps to keep my RAM requirements down a bit.
Perhaps that obvious/marginal suggestion might help for the time


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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