norm.quantile: Quantile normalization.

In xuz1/ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Quantile normalization.

Description

Quantile normalization of methylation intensity data across samples for Illumina Infinium HumanMethylation 450 and MethylationEPIC BeadChip.

Usage

norm.quantile(mdat, method = "quantile1")

Arguments

mdat	An object of class methDataSet or MethylSet.
method	Quantile normalization method: "quantile1", "quantile2", or "quantile3".

Details

By default, method = "quantile1", which will separately quantile normalize Methylated or Unmethylated intensities for Infinium I or II probes. The "quantile2" will quantile normalize combined Methylated or Unmethylated intensities for Infinium I or II probes. The "quantile3" will quantile normalize combined Methylated or Unmethylated intensities for Infinium I and II probes together.

Value

The output is an an object of class methDataSet or MethylSet.

Author(s)

Zongli Xu

References

Pidsley, R., CC, Y.W., Volta, M., Lunnon, K., Mill, J. and Schalkwyk, L.C. (2013) A data-driven approach to preprocessing Illumina 450K methylation array data. BMC genomics, 14, 293.

Examples

#for methDataSet
path <- file.path(find.package("minfiData"),"extdata")
rgSet <- readidat(path = path,recursive = TRUE)
mdat<-preprocessENmix(rgSet, bgParaEst="oob",nCores=6)
mdatq<-norm.quantile(mdat, method="quantile1")

#for MethySet
if (require(minfiData)) {
mdat=preprocessENmix(RGsetEx,bgParaEst="oob",nCores=6)
mdatq=norm.quantile(mdat,method="quantile1")
}

xuz1/ENmix documentation built on Aug. 5, 2023, 7:11 a.m.