preprocessENmix {ENmix} | R Documentation

## The ENmix background correction for HumanMethylation 450 and MethylationEPIC BeadChip

### Description

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 designs.

### Usage

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

### Arguments

`rgSet` | An object of class `RGChannelSetExtended`, `RGChannelSet` or `MethylSet`.
`bgParaEst` | Optional method to estimate background normal distribution parameters. This must be one of the strings: "oob","est", or "neg".
`dyeCorr` | Dye bias correction, "mean": correction based on averaged red/green ratio; or "RELIC": correction with RELIC method; or "none": no dye bias correction. The default is RELIC
`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 sample list to be excluded before background correction
`exCpG` | User specified probe list to be excluded before background correction
`nCores` | Number of cores will be used for computation

### Details

By default, ENmix will use out-of-band Infinium I intensities ("oob") to estimate normal distribution parameters to model 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.

### Value

An object of class `MethylSet`

### Author(s)

Zongli Xu and Liang Niu

### References

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, in review 2016

### Examples

    if(FALSE){
    if (require(minfiData)) {
    mdat=preprocessENmix(RGsetEx,nCores=6)
    }}

[Package ENmix version 1.21.6 Index]