batch_removal: batch_removal with sva's ComBat() function

In ShirinG/exprAnalysis: A package for analysing RNA-seq and expression array data

Description

Removes batch effects in combined datasets using sva's ComBat() function.

Usage

batch_removal(expmatrix, pheno)

Arguments

expmatrix	An input matrix with gene names as row names and sample names as column names.
pheno	Phenotype table with batch information.

Value

Returns batch corrected expression matrix.

Examples

test_expmatrix <- matrix(rnorm(100*30),nrow=100,ncol=8,
                         dimnames=list(c(rownames(expmatrix[1:100,1:8])),
                         c(colnames(expmatrix[1:100,1:8]))))
pheno <- data.frame(batch=as.factor(rep(c(1,2), 4)), row.names = colnames(test_expmatrix))
test_expmatrix <- batch_removal(expmatrix=test_expmatrix, pheno)

ShirinG/exprAnalysis documentation built on May 9, 2019, 1:28 p.m.