runLimmaBC: Apply Limma's batch effect correction method to...

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description

Limma's batch effect removal function fits a linear model to the data, then removes the component due to the batch effects.

Usage

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')
## Not run: 
sceCorr <- runLimmaBC(sceBatches)

## End(Not run)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.