funtooNorm {funtooNorm} | R Documentation

## The funtooNorm normalization function

### Description

`funtooNorm` Returns the normalized signals to the SampleSet object

### Usage

    funtooNorm(object, type.fits = "PCR", ncmp = 4, force = FALSE,
      sex = NULL)

    ## S4 method for signature 'SampleSet'
    funtooNorm(object, type.fits = "PCR", ncmp = 4,
      force = FALSE, sex = NULL)

### Arguments

`object` | Object of class SampleSet
`type.fits` | Choice between "PCR" or "PLS" (default="PCR")
`ncmp` | Number of components included in the analysis (default=4)
`force` | If set to TRUE, forces the normalization procedure to re-compute
`sex` | Boolean vector if male. if NULL Beta values from ChrY are used for classification.

### Details

This is a generic function which applies to autosomes and the X chromosome. Chromosome Y requires separate analysis as there are few probes on Y. We use a straightforward quantile normalization applied to males only.

### Value

a S4 object of class SampleSet containing the normalized signal

### Methods (by class)

- `SampleSet`: The funtooNorm normalization function

### Examples

    require(minfiData)
    pData(RGsetEx)$cell_type <- rep(c("type1","type2"),3)
    mySampleSet=fromRGChannelSet(RGsetEx)
    mySampleSet=funtooNorm(mySampleSet)

[Package funtooNorm version 1.18.0 Index]