normalize.quantile.450k: Quantile normalization.

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

Description

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

Usage

normalize.quantile.450k(mdat, method = "quantile1")

Arguments

mdat	An object of class MethylSet.
method	Quantile normalization method. This should be one of the following strings: "quantile1", "quantile2", or "quantile3".

Details

By default, method = "quantile1" 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

An object of class 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

if(FALSE){
if (require(minfiData)) {
mdat=preprocessENmix(RGsetEx,bgParaEst="oob",nCores=6)
mdatq1=normalize.quantile.450k(mdat,method="quantile1")
}}

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