norm.quantile: Quantile normalization.

Description Usage Arguments Details Value Author(s) References Examples

View source: R/norm.quantile.R

Description

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

Usage

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norm.quantile(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

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

ENmix documentation built on May 2, 2018, 4:24 a.m.