Hi Chuck, On Mon, Oct 11, 2010 at 11:24 AM, Charles C. Berry <[email protected]> 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 being? -steve -- 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
