batchEffectRemoval: Corrects the batch effect of the data by using the selected...
In KnowSeq: KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Description Usage Arguments Value Examples

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

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

`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.

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

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