batchRemove: Elimination of covariates batch effect or bias

In Juananvg/DExMA: Differential Expression Meta-Analysis

Elimination of covariates batch effect or bias

Description

It eliminates the effects of batch or bias of the covariates

Usage

batchRemove(expressionMatrix, pheno, formula, mainCov = NULL, nameGroup, ...)

Arguments

expressionMatrix	A matrix or data frame with genes in rows and samples in columns. An ExpressionSet object can be used too
pheno	A dataframe with samples in rows and covariates in colums.
formula	Formula of the covariates that are wanted to be corrected
mainCov	Name of the main covariate to be corrected
nameGroup	Name of the column of the Phenodata object in which the reference groups (cases and controls) are
...	other arguments are passed to lmFit fucntion of limma package

Value

The Expression Matrix with the bias or batch effect corrected. Moreover a plot of the visualization of the association between principal components and covariates is shown.

Author(s)

Juan Antonio Villatoro Garcia, [e-mail]

References

Martin Lauss (2019). swamp: Visualization, Analysis and Adjustment of High-Dimensional Data in Respect to Sample Annotations. R package version 1.5.1. https://CRAN.R-project.org/package=swamp

Examples

data(DExMAExampleData)
batchRemove(listMatrixEX$Study2, listPhenodatas$Study2, formula=~gender+race,
nameGroup="condition")

Juananvg/DExMA documentation built on Dec. 5, 2023, 1:12 p.m.