[Bioc-devel] Incrimental writing to HDF5 / DelayedMatrix

Francesco Napolitano franapoli at gmail.com
Thu Dec 21 14:08:30 CET 2017

Thank you very much, Paul, I'll have a look at your code.


On Thu, Dec 21, 2017 at 1:01 PM, Paul Theodor Pyl
<paul.theodor.pyl at embl.de> wrote:
> Hi Francesco,
> this is certainly achievable with currently available HDF5 support in
> R/Bioconductor. For example the rhdf5 package gives you access to this
> functionality
> (https://bioconductor.org/packages/release/bioc/html/rhdf5.html).
> rhdf5 is relatively 'low-level', in the sense that it is really close to the
> HDF5 library it exposes to R (i.e. you get h5read an h5write functions). For
> what you are describing I typically use a small wrapper to make my life a
> bit easier, I have something like that on github here:
> https://github.com/PaulPyl/h5array
> Please note that this is not an official Bioconductor package so it doesn't
> fulfill the strict standards of documentation etc., since it is just a small
> wrapper to give you an array-like object that writes/reads its data from
> disk though, it should be fairly straightforward to use.
> Best,
> Paul
> On Thu, Dec 21, 2017 at 12:22, Francesco Napolitano <franapoli at gmail.com>
> wrote:
> Hi,
> I need to deal with very large matrices and I was thinking of using
> HDF5-based data models. However, from the documentation and examples
> that I have been looking at, I'm not quite sure how to do this.
> My use case is as follows.
> I want to build a very large matrix one column at a time, and I need
> to write columns directly to disk since I would otherwise run out of
> memory. I need a format that, afterwards, will allow me to extract
> subsets of rows or columns and rank them. The subsets will be small
> enough to be loaded in memory. Can I achieve this with current HDF5
> support in R?
> Any help greatly appreciated.
> than you,
> Francesco
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