ComBat.mc: A multi-processor wrapper for ComBat method.

In USCbiostats/ENmixUSC: Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

Description

A multi-processor wrapper for ComBat method. ComBat is a method to adjust batch effect where the batch covariate is known.

Usage

ComBat.mc(dat,batch,nCores = 1,...)

Arguments

dat	A data matrix with column for samples and row for probe.
batch	Batch covariate (multiple batches allowed)
nCores	Number of cores will be used for computation
...	See ComBat in sva package for extra options

Value

A data matrix with the same dimension as input data, adjusted for batch effects. Warning: Values for multimodal distributed CpGs could be over-adjusted.

Author(s)

Zongli Xu

References

Johnson, WE, Rabinovic, A, and Li, C (2007). Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8(1):118-127.

See Also

See ComBat in sva package for details.

Examples

if(FALSE){
if (require(minfiData)) {
mdat=preprocessENmix(RGsetEx,bgParaEst="oob",nCores=6)
mdat=norm.quantile(mdat,method="quantile1")
beta=bmiq.mc(mdat,nCores=10)
batch=factor(pData(mdat)$Slide)
betaC=ComBat.mc(beta,batch,nCores=6,mod=NULL)
}}

USCbiostats/ENmixUSC documentation built on June 1, 2019, 3:55 a.m.