funtooNorm: The funtooNorm normalization function

In GreenwoodLab/funtooNorm: Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit

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)

GreenwoodLab/funtooNorm documentation built on April 5, 2022, 3:22 p.m.