BatchRemove {MAGeCKFlute}R Documentation

Batch effect removal

Description

Remove batch effect

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, which has at least two columns, including Samples(matched colname of mat) and Batch. It can have the third column, which should be Covariate.

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(MLE_Data)
beta = ReadBeta(MLE_Data, organism="hsa")
samples = c("D7_R1", "D7_R2", "PLX7_R1", "PLX7_R2")
batchMat = data.frame(samples = samples, batch = c("bat1","bat2","bat1","bat2"), cov = c(1,1,2,2))
res = BatchRemove(beta[, samples], batchMat)


[Package MAGeCKFlute version 1.0.1 Index]