batchEffectRemoval {KnowSeq} | R Documentation

## Corrects the batch effect of the data by using the selected method.

### Description

This function corrects the batch effect of the expression matrix indicated by parameter. There are two method to choose such as ComBat or SVA.

### Usage

    batchEffectRemoval(
      expressionMatrix,
      labels,
      method = "combat",
      batchGroups = c()
    )

### Arguments

`expressionMatrix` | The original expression matrix to treat the batch effect.
`labels` | A vector that contains the labels of the samples in expressionMatrix.
`method` | The method that will be used to remove the batch effect. The possibilities are "combat" or "sva". Next release will add RUV.
`batchGroups` | A numeric vector with the different known batch groups for the samples.

### Value

A matrix with the batch effect corrected for combat or a model for `DEGsExtraction` function in the case of sva.

### Examples

    dir <- system.file("extdata", package="KnowSeq")
    load(paste(dir,"/expressionExample.RData",sep = ""))

    batchGroups <- c(1,1,1,1,2,2,1,2,1,2)

    expressionMatrixNoBatch <- batchEffectRemoval(expressionMatrix, labels, batchGroups = batchGroups)
    svaMod <- batchEffectRemoval(expressionMatrix, labels, method = "sva")

[Package KnowSeq version 1.1.27 Index]