preprocessENmix: The ENmix background correction for HumanMethylation 450 and...

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

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

See Also

Package minfi for classes RGChannelSet and MethylSet

Examples

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

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