lumi (version 2.24.0)

normalizeMethylation.quantile: Quantile normalization of Illumina Infinium methylation data at probe level

Description

Quantile normalization of Illumina Infinium methylation data at probe level. Input data is a MethyLumiM object

Usage

normalizeMethylation.quantile(methyLumiM, separateColor = FALSE, reference = NULL, ...)

Arguments

methyLumiM

a MethyLumiM object includes Illumina Infinium methylation data

separateColor

determine whether separately normalize two color channels

reference

the reference vector (same length as the number of matrix rows) for quanitle normalization

...

other parameters used by normalize.quantiles.robust method

Value

Return an object (same class as input methyLumiM) with updated "methylated" and "unmethylated" data matrix after background level adjustment.

See Also

See Also lumiMethyN, and normalizeMethylation.ssn

Examples

data(example.lumiMethy)
lumiMethy.norm = normalizeMethylation.quantile(example.lumiMethy)