ComBatWrapper: Wrapper for the ComBat.R function

In lwaldron/LeviRmisc: Levi's miscellaneous handy R functions

Description

Applies the ComBat batch correction algorithm without having to manually create the input files. Function by Levi Waldron.

Usage

ComBatWrapper(expr.uncorrected, batchvar, combat.source = "http://www.bu.edu/jlab/wp-assets/ComBat/Download_files/ComBat.R", 
    cleanup = TRUE, ...)

Arguments

expr.uncorrected	A matrix of uncorrected expression values, with samples in columns and features in rows
batchvar	A character string of length equal to the number of columns in expr.uncorrected, defining the batches
combat.source	A location where the ComBat.R script can be found
cleanup	If TRUE, clean up intermediate files when done
...	... are extra arguments passed to the ComBat function

Value

a matrix of batch-corrected values, of the same dimensions as the input expr.uncorrected. Note that this script also makes a plot, unless prior.plots=FALSE is passed in the ...

Author(s)

Levi Waldron and Markus Riester

lwaldron/LeviRmisc documentation built on May 21, 2019, 8:59 a.m.