View source: R/runBatchCorrection.R
runLimmaBC | R Documentation |
Limma's batch effect removal function fits a linear model to the data, then removes the component due to the batch effects.
runLimmaBC(inSCE, useAssay = "logcounts", assayName = "LIMMA", batch = "batch")
inSCE |
Input SingleCellExperiment object |
useAssay |
A single character indicating the name of the assay requiring
batch correction. Default |
assayName |
A single characeter. The name for the corrected assay. Will
be saved to |
batch |
A single character indicating a field in |
The input SingleCellExperiment object with
assay(inSCE, assayName)
updated.
Gordon K Smyth, et al., 2003
data('sceBatches', package = 'singleCellTK')
logcounts(sceBatches) <- log1p(counts(sceBatches))
sceCorr <- runLimmaBC(sceBatches)
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