multiGSEA
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Add support to handle (sparse) Matrix expression objects
When we're playing with single cell data, some methods get tripped up when the expression-like matrix is a sparse Matrix
, ie. a dgCMatrix
.
We need to fix this. One option would be to more often use the functions in DelayedMatrixStats
on an object you wrap with DelayedArray()
, I think, eg. DelayedMatrixStats::DelayedArray(counts(sce))
I think should work, but this takes a long time. Let's be smart about this.
Code that is effected:
- [ ]
scoreSingleSamples()
: we are explicitly convertingsparseMatrix
with `as.matrix() - [ ]
mgheatmap
: Also test forsparseMatrix
and explicitly convert to dense before centering / scaling.