mpreprocess {ENmix} | R Documentation

## A pipeline to perform background correction, dye bias correction, inter-array normalization and probe type bias correction for HumanMethylation 450 and MethylationEPIC BeadChip data.

### Description

Fuction mpreprocess is a pipeline to easy preprocess steps for Illumina DNA methylation BeadChip. It comprehensively removes background noise and correct bias due to array design, including background correction, dye bias correction, inter-array normalization, probe type bias correction. It will also identify and exclude low quality samples and probes, remove outlier values, and perform imputation.

### Usage

        mpreprocess(rgSet,nCores=1,bgParaEst="oob",dyeCorr="RELIC",
                    qc=FALSE,qnorm=TRUE,qmethod="quantile1",
                    foutlier=TRUE,rmcr=FALSE,impute=FALSE)

### Arguments

`rgSet` | An object of class `rgDataSet`,`methDataSet`, `RGChannelSetExtended`, `RGChannelSet` or `MethylSet`.
`nCores` | Number of cores will be used for computation
`bgParaEst` | 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
`qc` | If TRUE, QC will be performed. Low quality samples and CpGs will be excluded before background correction.
`qnorm` | If TRUE, inter-array quantile normalization will be performed.
`qmethod` | Quantile normalization method. This should be one of the following strings: "quantile1", "quantile2", or "quantile3". See details in function norm.quantile.
`foutlier` | If TRUE, outlier and low quality values will be filtered out.
`rmcr` | TRUE: excluded rows and columns with more than 5% of missing values. FALSE is in default
`impute` | Whether to impute missing values. If TRUE, k-nearest neighbor's methods will be used for imputation. FALSE is in default.

### Details

Fuction mpreprocess is a pipeline that perform methylaiton data preprocessing and quality controls using functions: preprocessENmix, norm.quantile, rcp, QCinfo and rm.outlier. More customized preprocessing steps can be achieved using the individual functions.

### Value

a methylation beta value matrix.

### Author(s)

Zongli Xu

### 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

Liang Niu, Zongli Xu and Jack A. Taylor: RCP: a novel probe design bias correction method for Illumina Methylation BeadChip, Bioinformatics 2016

### See Also

Package `minfi` for classes `RGChannelSet` and `MethylSet`

### Examples

    if(FALSE){
    if (require(minfiData)) {
    beta=mpreprocess(RGsetEx,nCores=6)

    sheet <- read.metharray.sheet(file.path(find.package("minfiData"),"extdata"), pattern = "csv$")
    rgSet <- read.metharray.exp(targets = sheet,extended = TRUE)
    beta=mpreprocess(rgSet,nCores=6,qc=TRUE,foutlier=TRUE,rmcr=TRUE,impute=TRUE)
    }}

[Package ENmix version 1.21.6 Index]