ENmix (version 1.8.0)

preprocessENmix: 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=TRUE, 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: "TRUE" or "FALSE"

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

Value

An object of class MethylSet

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.

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.

See Also

Package minfi for classes RGChannelSet and MethylSet

Examples

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