runLimmaBC {singleCellTK} | 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 |
SingleCellExperiment inherited object. Required. |
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) <- log(counts(sceBatches) + 1) sceCorr <- runLimmaBC(sceBatches)