runLimmaBC {singleCellTK} | R Documentation

## Apply Limma's batch effect correction method to SingleCellExperiment object

### 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')
    logcounts(sceBatches) <- log(counts(sceBatches) + 1)
    sceCorr <- runLimmaBC(sceBatches)

[Package singleCellTK version 2.2.0 Index]