[Bioc-devel] pointer and big matrix in R

Vincent Carey stvjc at channing.harvard.edu
Fri Apr 12 19:14:44 CEST 2013

for some approaches to working with large matrices in R, please look at


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.Servant at 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
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