lumiMethyN {lumi} | R Documentation

## Normalize the Illumina Infinium methylation data

### Description

Normalize the Illumina Infinium methylation data, which is an object in MethyLumiM class.

### Usage

    lumiMethyN(methyLumiM, method = c("quantile", "ssn", "none"), separateColor = FALSE, verbose = TRUE, overwriteBigMatrix = FALSE, ...)

### Arguments

`methyLumiM` | a MethyLumiM object includes Illumina Infinium methylation data
`method` | supported normalization methods or user provided function, whose input and output should be a intensity matrix (pool of methylated and unmethylated probe intensities)
`separateColor` | determine whether to separately process two color channels
`verbose` | a boolean to decide whether to print out some messages
`overwriteBigMatrix` | whether to overwrite the result to the BigMatrix data, only valid when the input data is BigMatrix-based
`...` | other parameters used by corresponding 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 `normalizeMethylation.ssn` and `normalizeMethylation.quantile`

### Examples

    data(example.lumiMethy)
    lumiMethy.norm = lumiN(example.lumiMethy)

[Package lumi version 2.44.0 Index]