runFastMNN {singleCellTK} | R Documentation |
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
## Not run: data('sceBatches', package = 'singleCellTK') sceCorr <- runFastMNN(sceBatches, useAssay = 'logcounts', pcInput = FALSE) ## End(Not run)