batchRemove {DExMA}R Documentation

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

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.

Note

For more information of the returned visualization see the seeCOV function

Author(s)

Juan Antonio Villatoro Garcia, juanantoniovillatorogarcia@gmail.com

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

See Also

seeCov

Examples

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


[Package DExMA version 1.0.2 Index]