for some approaches to working with large matrices in R, please look at http://cran.r-project.org/web/views/HighPerformanceComputing.html
scroll down to "Large memory and out-of-memory data" i suspect this view text should be enlarged to include rhdf5 and ncdf as additional relevant resources On Fri, Apr 12, 2013 at 1:02 PM, Servant Nicolas <nicolas.serv...@curie.fr> wrote: > > Dear all, > > I have a S4 object (HTCexp from HITC package), composed of one big matrix, > and two genomicRanges objects, A and B which describe the matrix raws and > columns. > I thinking about a way to decrease the memory size of this object. > I also have methods to get/set the matrix and the two GRanges, namely > intdata(), x_intervals(), y_intervals(). > > In case of symetric matrix, the two GRanges can be the same, so I was > interested in simply creating in this case, a pointer from B to A. How can I > do it in R please ?? > Second, I'm wondering if it exists other matrix-like object optimized for big > matrix (5000 x 5000). I quicky saw the Matrix object from the CRAN, useful > for sparse matrix. > Any suggestion would be appreciated ! > > Thank you > Regards > Nicolas > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
