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Add support to handle (sparse) Matrix expression objects

Open lianos opened this issue 6 years ago • 0 comments

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 converting sparseMatrix with `as.matrix()
  • [ ] mgheatmap: Also test for sparseMatrix and explicitly convert to dense before centering / scaling.

lianos avatar Dec 18 '18 05:12 lianos