ComBat: Adjust for batch effects using an empirical Bayes framework

In steveneschrich/msva: Surrogate Variable Analysis

Description

ComBat allows users to adjust for batch effects in datasets where the batch covariate is known, using methodology described in Johnson et al. 2007. It uses either parametric or non-parametric empirical Bayes frameworks for adjusting data for batch effects. Users are returned an expression matrix that has been corrected for batch effects. The input data are assumed to be cleaned and normalized before batch effect removal.

Usage

ComBat(
  dat,
  batch,
  mod = NULL,
  par.prior = TRUE,
  prior.plots = FALSE,
  mean.only = FALSE,
  ref.batch = NULL,
  BPPARAM = bpparam("SerialParam")
)

Arguments

dat	Genomic measure matrix (dimensions probe x sample) - for example, expression matrix
batch	Batch covariate (only one batch allowed)
mod	Model matrix for outcome of interest and other covariates besides batch
par.prior	(Optional) TRUE indicates parametric adjustments will be used, FALSE indicates non-parametric adjustments will be used
prior.plots	(Optional) TRUE give prior plots with black as a kernel estimate of the empirical batch effect density and red as the parametric
mean.only	(Optional) FALSE If TRUE ComBat only corrects the mean of the batch effect (no scale adjustment)
ref.batch	(Optional) NULL If given, will use the selected batch as a reference for batch adjustment.
BPPARAM	(Optional) BiocParallelParam for parallel operation

Value

data A probe x sample genomic measure matrix, adjusted for batch effects.

Examples

library(bladderbatch)
data(bladderdata)
dat <- bladderEset[1:50,]

pheno = pData(dat)
edata = exprs(dat)
batch = pheno$batch
mod = model.matrix(~as.factor(cancer), data=pheno)

# parametric adjustment
combat_edata1 = ComBat(dat=edata, batch=batch, mod=NULL, par.prior=TRUE, prior.plots=FALSE)

# non-parametric adjustment, mean-only version
combat_edata2 = ComBat(dat=edata, batch=batch, mod=NULL, par.prior=FALSE, mean.only=TRUE)

# reference-batch version, with covariates
combat_edata3 = ComBat(dat=edata, batch=batch, mod=mod, par.prior=TRUE, ref.batch=3)

steveneschrich/msva documentation built on Dec. 23, 2021, 5:33 a.m.