R/runBatchCorrection.R
runFastMNN.Rd
fastMNN is a variant of the classic MNN method, modified for speed and more
robust performance. For introduction of MNN, see runMNNCorrect
.
runFastMNN( inSCE, useAssay = "logcounts", reducedDimName = "fastMNN", batch = "batch", pcInput = FALSE )
inSCE | inherited object. Required. |
---|---|
useAssay | A single character indicating the name of the assay requiring
batch correction. Default |
reducedDimName | A single character. The name for the corrected
low-dimensional representation. Will be saved to |
batch | A single character indicating a field in
|
pcInput | A logical scalar. Whether to use a low-dimension matrix for
batch effect correction. If |
The input SingleCellExperiment object with
reducedDim(inSCE, reducedDimName)
updated.
Lun ATL, et al., 2016
data('sceBatches', package = 'singleCellTK') logcounts(sceBatches) <- log(counts(sceBatches) + 1) sceCorr <- runFastMNN(sceBatches, useAssay = 'logcounts', pcInput = FALSE)#> Warning: You're computing too large a percentage of total singular values, use a standard svd instead.