preprocessENmix: The ENmix background correction
In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description Usage Arguments Details Value Author(s) References Examples

The ENmix background correction for HumanMethylation 450 and MethylationEPIC BeadChip. ENmix models methylation signal intensities with a flexible exponential-normal mixture distribution, and models background noise with a truncated normal distribution. ENmix will split BeadChip intensity data into 6 parts and separately model methylated and unmethylated intensities, 2 different color channels and 2 different probe types.

1 2	preprocessENmix(rgSet, bgParaEst = "oob", dyeCorr="RELIC", QCinfo=NULL, exQCsample=TRUE, exQCcpg=TRUE, exSample=NULL, exCpG=NULL, nCores = 2)

`rgSet`	An object of class `rgDataSet`, `methDataSet`, `RGChannelSetExtended`, `RGChannelSet` or `MethylSet`.
`bgParaEst`	Method to estimate background normal distribution parameters. Options are: "oob","est", or "neg".
`dyeCorr`	Dye bias correction method, "mean": correction based on averaged red/green ratio, or "RELIC": correction with RELIC method (default method), or "none": no dye bias correction.
`QCinfo`	If QCinfo object from function QCinfo() is provided, low quality samples (if exQCsample=TRUE) and CpGs (if exQCcpg=TRUE) will be excluded before background correction.
`exQCsample`	If TRUE, low quality samples listed in QCinfo will be excluded.
`exQCcpg`	If TRUE, low quality CpGs listed in QCinfo will be excluded.
`exSample`	User specified samples to be excluded before background correction
`exCpG`	User specified probes to be excluded before background correction
`nCores`	Number of cores will be used for computation

By default, ENmix will use out-of-band Infinium I intensities ("oob") to estimate normal distribution parameters for modeling background noise. Option "est" will use combined methylated and unmethylated intensities to estimate background distribution parameters separately for each color channel and each probe type. Option "neg" will use 600 chip internal controls probes to estimate background distribution parameters. If rgSet if a MethylSet, then only option "est" can be selected.

An object of class same with input data

Zongli Xu and Liang Niu

Zongli Xu, Liang Niu, Leping Li and Jack A. Taylor, ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic Acids Research 2015.

Zongli Xu, Sabine A. S. Langie, Patrick De Boever, Jack A. Taylor1 and Liang Niu, RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip, BMC Genomics. 2017

if (require(minfiData)) {
#rgDataSet as input
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
#quality control information
qc<-QCinfo(rgSet)
#further excluding samples which are not in the qc$badsample list
ex_id=c("5723646053_R04C02")
#further excluding cpgs which are not in the qc$badCpG list
ex_cg=c("cg00000622", "cg00001245", "cg00001261")
mdat=preprocessENmix(rgSet,QCinfo=qc,exSample=ex_id,exCpG=ex_cg,nCores=6)


#RGChannelSet as input
mdat=preprocessENmix(RGsetEx,nCores=6)
}