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

Aaron Lun alun at wehi.edu.au
Fri Feb 24 22:26:51 CET 2017

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.



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