normalizeMethylation.quantile {lumi} | R Documentation

## 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.

### Author(s)

Pan DU

### See Also

See Also `lumiMethyN`, and `normalizeMethylation.ssn`

### Examples

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

[Package lumi version 2.40.0 Index]