norm.quantile: Quantile normalization.
In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description Usage Arguments Details Value Author(s) References Examples

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

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

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

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.

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

Zongli Xu

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.

#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")
}