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MarioniLab / scran

Clone of the Bioconductor repository for the scran package.
https://bioconductor.org/packages/devel/bioc/html/scran.html
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Add a fixedPCA function to avoid relying on scater::runPCA #84

Closed LTLA closed 3 years ago

LTLA commented 3 years ago

Doesn't make sense to have to loop out to scater for such a common step.

Also add warnings when subset.row= is not explicitly specified (either as some valid value or NULL). Probably like:

## Warning: 
## no 'subset.row=' has been specified for feature selection prior to PCA.
## If this is intentional, set 'subset.row=NULL' to remove this warning.
LTLA commented 3 years ago

Added fixedPCA in f6cdc261c51942dce9b809181cf6a79dfdb37f03.

Note to self, need to add a preserve.shape= option in denoisePCA.