mtmorgan / TENxGenomics

Interface to 10x Genomics' 1.3 m single cell data set
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Proof of concept of coercion to sparse matrix #3

Closed PeteHaitch closed 7 years ago

PeteHaitch commented 7 years ago

Proof of concept to show the efficiency of using the sparse representation.

As commented in the source code, this uses a dgCMatrix, a compressed, sparse, column-oriented numeric (double) matrix from the Matrix package. What we really want to use to store these data is a igCMatrix, a compressed, sparse, column-oriented integer matrix. However, the igCMatrix class, while defined in the Matrix package, is not actually implemented. Matrix is in DEPENDS because you can't do much with the returned object otherwise (I think).

These changes caused some havoc with roxygen, so I needed to do some manual editing. I'll try to figure out the source and fix so this doesn't have to be done each time.

Also, where can I obtain v2.19.3-2 of rhdf5? Can't see it on Github.

mtmorgan commented 7 years ago

I pushed rhdf5 so should be available now; I'll incorprate a refactored version of this pull request in the not too distant future, thanks!