R/runBatchCorrection.R
runLimmaBC.Rd
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")
Input SingleCellExperiment object
A single character indicating the name of the assay requiring
batch correction. Default "logcounts"
.
A single characeter. The name for the corrected assay. Will
be saved to assay
. Default
"LIMMA"
.
A single character indicating a field in colData
that
annotates the batches of each cell; or a vector/factor with the same length
as the number of cells. Default "batch"
.
The input SingleCellExperiment object with
assay(inSCE, assayName)
updated.
Gordon K Smyth, et al., 2003