[Bioc-devel] any interest in a BiocMatrix core package?

[Vincent Carey]

Kylie, thanks for reminding us of matter -- I saw you speak about this at
the first Bioconductor Boston Meetup, but it
went like lightning.   For developers contemplating an approach to
representing high-volume rectangular data,
where there is no dominant legacy format, it is natural to wonder whether
HDF5 would be adequate, and,
further, to wonder how to demonstrate that it is or is not dominated by
some other approach for a given set
of tasks.  Should we devise a set of bioinformatic benchmark problems to
foster comparison and informed
decisionmaking?  @becker.gabe: is ALTREP far enough along that one could
contemplate benchmarking with it?

On Fri, Feb 24, 2017 at 7:08 PM, Bemis, Kylie <k.bemis at northeastern.edu>
wrote:

> It’s not there yet, but I plan to expose a C++ API for my disk-backed
> matrix objects in the next version of my ‘matter’ package.
>
> It’s getting easier to interchange matter/HDF5Array/bigmemory/etc.
> objects at the R level, especially if using a frontend like DelayedArray on
> top of them, but it would be nice to have a common C++ API that I could
> hook into as well (a la Rcpp), so new C/C++ could be re-used across various
> backends more easily.
>
> Kylie
>
> ~~~
> Kylie Ariel Bemis
> Future Faculty Fellow
> College of Computer and Information Science
> Northeastern University
> kuwisdelu.github.io<https://kuwisdelu.github.io>
>
>
>
>
> On Feb 24, 2017, at 4:50 PM, Aaron Lun <alun at wehi.edu.au<mailto:alun@
> wehi.edu.au>> wrote:
>
> It's a good place to start, though it would be very handy to have a C(++)
> API that can be linked against. I'm not sure how much work that would
> entail but it would give downstream developers a lot more options. Sort of
> like how we can link to Rhtslib, which speeds up a lot of BAM file
> processing, instead of just relying on Rsamtools.
>
>
> -Aaron
>
> ________________________________
> From: Tim Triche, Jr. <tim.triche at gmail.com<mailto:tim.triche at gmail.com>>
> Sent: Saturday, 25 February 2017 8:34:58 AM
> To: Aaron Lun
> Cc: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
> Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package?
>
> yes
>
> the DelayedArray framework that handles HDF5Array, etc. seems like the
> right choice?
>
> --t
>
> On Fri, Feb 24, 2017 at 1:26 PM, Aaron Lun <alun at wehi.edu.au<mailto:alun@
> wehi.edu.au><mailto:alun at wehi.edu.au>> wrote:
> Hi everyone,
>
> I just attended the Human Cell Atlas meeting in Stanford, and people were
> talking about gene expression matrices for >1 million cells. If we assume
> that we can get non-zero expression profiles for ~5000 genes, we�d be
> talking about a 5000 x 1 million matrix for the raw count data. This would
> be 20-40 GB in size, which would clearly benefit from sparse (via Matrix)
> or disk-backed representations (bigmatrix, BufferedMatrix, rhdf5, etc.).
>
> I�m wondering whether there is any appetite amongst us for making a
> consistent BioC API to handle these matrices, sort of like what
> BiocParallel does for multicore and snow. It goes without saying that the
> different matrix representations should have consistent functions at the R
> level (rbind/cbind, etc.) but it would also be nice to have an integrated
> C/C++ API (accessible via LinkedTo). There�s many non-trivial things that
> can be done with this type of data, and it is often faster and more memory
> efficient to do these complex operations in compiled code.
>
> I was thinking of something that you could supply any supported matrix
> representation to a registered function via .Call; the C++ constructor
> would recognise the type of matrix during class instantiation; and
> operations (row/column/random read access, also possibly various ways of
> writing a matrix) would be overloaded and behave as required for the class.
> Only the implementation of the API would need to care about the nitty
> gritty of each representation, and we would all be free to write code that
> actually does the interesting analytical stuff.
>
> Anyway, just throwing some thoughts out there. Any comments appreciated.
>
> Cheers,
>
> Aaron
>
>        [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org><mailto:
> Bioc-devel at r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]