BatchRemove {MAGeCKFlute}R Documentation

Batch effect removal

Description

Batch effect removal

Usage

BatchRemove(mat, batchMat, log2trans = FALSE, positive = FALSE)

Arguments

mat

Matrix, or a file path of data.

batchMat

Matrix like data object or a file path of batch table, in which the first two columns are 'Samples'(matched colname of mat) and 'Batch', and remaining columns should be Covariates.

log2trans

Boolean, specifying whether do log2 transition before batch removal.

positive

Boolean, specifying whether all values should be positive.

Value

A list contrains two objects, including data and p.

Author(s)

Wubing Zhang

See Also

ComBat

Examples

data(bladderdata, package = "bladderbatch")
dat <- bladderEset[1:50,]
pheno = pData(dat)
edata = exprs(dat)
batchMat = pheno[, c("sample", "batch", "cancer")]
batchMat$sample = rownames(batchMat)
edata1 = BatchRemove(edata, batchMat)


[Package MAGeCKFlute version 1.2.3 Index]