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

[Wolfgang Huber]

Aaron

Can you describe use cases, i.e. intended computations on these 
matrices, esp. those for which C++ access is needed for?

I'm asking b/c the goals of efficient code and abstraction from how the 
data are stored may be conflicting - in which case critical algorithms 
may end up circumventing a prematurely defined API.

Wolfgang


25.2.17 00:37, Aaron Lun scripsit:
> Yes, I think double-precision would be necessary for general use. Only the raw count data would be integer, and even then that's not guaranteed (e.g., if people are using kallisto or salmon for quantification).
>
>
> -Aaron
>
>
> ________________________________
> From: Vincent Carey <stvjc at channing.harvard.edu>
> Sent: Saturday, 25 February 2017 9:25 AM
> To: Aaron Lun
> Cc: Tim Triche, Jr.; bioc-devel at r-project.org
> Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package?
>
> What is the data type for an expression value?  Is it assumed that double precision will be needed?
>
> On Fri, Feb 24, 2017 at 4:50 PM, Aaron Lun <alun at wehi.edu.au<mailto:alun at 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 at wehi.edu.au><mailto:alun at 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,
>