# Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit

## Documentation for package ‘funtooNorm’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

funtooNorm-package | funtooNorm
agreement | Function to measure intra-replicate agreement for methylation data.
fromGenStudFiles | Creates a S4 object of class 'SampleSet' from GenomeStudio files
fromRGChannelSet | Creates an object of class SampleSet from a RGChannelSet minfi
funtooNorm | The funtooNorm normalization function
funtooNorm-method | The funtooNorm normalization function
getGRanges | Build GRange object of methylation probes
getGRanges-method | Build GRange object of methylation probes
getNormBeta | Computes Beta values from normalized signals
getNormBeta-method | Computes Beta values from normalized signals
getNormM | Computes M values,log2(Meth/Unmeth), from normalized signals
getNormM-method | Computes M values,log2(Meth/Unmeth), from normalized signals
getRawBeta | Computes Beta value from raw signals
getRawBeta-method | Computes Beta value from raw signals
getSnpM | Computes M values after normalization of SNP data.
getSnpM-method | Computes M values after normalization of SNP data.
plotValidationGraph | plot of Validation Graph for determing number of components
plotValidationGraph-method | plot of Validation Graph for determing number of components
SampleSet-class | S4 class object SampleSet
show-method | Show Object SampleSet