Apply Limma's batch effect correction method to SingleCellExperiment object

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")

Arguments

inSCE

SingleCellExperiment inherited object. Required.

useAssay

A single character indicating the name of the assay requiring batch correction. Default "logcounts".

assayName

A single characeter. The name for the corrected assay. Will be saved to assay. Default "LIMMA".

batch

A single character indicating a field in colData that annotates the batches. Default "batch".

Value

The input SingleCellExperiment object with assay(inSCE, assayName) updated.

References

Gordon K Smyth, et al., 2003

Examples

data('sceBatches', package = 'singleCellTK')
logcounts(sceBatches) <- log(counts(sceBatches) + 1)
sceCorr <- runLimmaBC(sceBatches)