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
)
inherited object. Required.
A single character indicating the name of the assay requiring
batch correction. Default "logcounts"
. Alternatively, see
pcInput
parameter.
A single character. The name for the corrected
low-dimensional representation. Will be saved to reducedDim(inSCE)
.
Default "fastMNN"
.
A single character indicating a field in
colData
that annotates the batches.
Default "batch"
.
A logical scalar. Whether to use a low-dimension matrix for
batch effect correction. If TRUE
, useAssay
will be searched
from reducedDimNames(inSCE)
. Default FALSE
.
The input SingleCellExperiment object with
reducedDim(inSCE, reducedDimName)
updated.
Lun ATL, et al., 2016