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")

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