batchCorrectionAssay {MatrixQCvis} | R Documentation

## Remove batch effects from (count/intensity) values of a 'SummarizedExperiment'

### Description

The function 'batchCorrectionAssay' removes the batch effect of (count/intensity) values of a 'SummarizedExperiment'. It uses either the 'removeBatchEffect' function or no batch effect correction method (pass-through, 'none').

### Usage

    batchCorrectionAssay(
      se,
      method = c("none", "removeBatchEffect (limma)"),
      batchColumn = colnames(colData(se))
    )

### Arguments

`se` | 'SummarizedExperiment'
`method` | 'character', one of '"none"' or '"removeBatchEffect"'
`batchColumn` | 'character', one of 'colnames(colData(se))'

### Details

The column 'batchColumn' in 'colData(se)' contains the information on the batch identity. Internal use in 'shinyQC'.

### Value

'matrix'

### Examples

    ## create se
    a <- matrix(1:100, nrow = 10, ncol = 10,
                dimnames = list(1:10, paste("sample", 1:10)))
    a[c(1, 5, 8), 1:5] <- NA
    set.seed(1)
    a <- a + rnorm(100)
    cD <- data.frame(name = colnames(a),
        type = c(rep("1", 5), rep("2", 5)), batch = rep(c(1, 2), 5))
    rD <- data.frame(spectra = rownames(a))
    se <- SummarizedExperiment::SummarizedExperiment(assay = a,
        rowData = rD, colData = cD)

    batchCorrectionAssay(se, method = "removeBatchEffect (limma)",
                                batchColumn = "batch")

[Package MatrixQCvis version 1.0.0 Index]