GenomicMethylSet-class
                        GenomicMethylSet instances
IlluminaMethylationAnnotation-class
                        Class 'IlluminaMethylationAnnotation'
IlluminaMethylationManifest-class
                        Class '"IlluminaMethylationManifest"'
MethylSet-class         MethylSet instances
RGChannelSet-class      Class '"RGChannelSet"'
controlStripPlot        Plot control probe signals.
densityBeanPlot         Density bean plots of methylation Beta values.
densityPlot             Density plots of methylation Beta values.
detectionP              Detection p-values for all probed genomic
                        positions.
dmpFinder               Find differentially methylated positions
logit2                  logit in base 2.
mapToGenome-methods     Mapping methylation data to the genome
mdsPlot                 Multi-dimensional scaling plots giving an
                        overview of similarities and differences
                        between samples.
minfi-package           Analyze Illumina's methylation arrays
plotBetasByType         Plot the overall distribution of beta values
                        and the distributions of the Infinium I and II
                        probe types.
plotCpg                 Plot methylation values at an single genomic
                        position
preprocessIllumina      Perform preprocessing as Genome Studio.
preprocessRaw           Creation of a MethylSet without normalization
preprocessSWAN          Subset-quantile Within Array Normalisation for
                        Illumina Infinium HumanMethylation450 BeadChips
qcReport                QC report for Illumina Infinium Human
                        Methylation 450k arrays
read.450k               Parsing IDAT files from Illumina methylation
                        arrays.
read.450k.exp           Reads an entire 450k experiment using a sample
                        sheet
read.450k.sheet         Reading an Illumina methylation sample sheet
