GenomicMethylSet-class
                        GenomicMethylSet instances
GenomicRatioSet-class   GenomicRatioSet instances
IlluminaMethylationAnnotation-class
                        Class 'IlluminaMethylationAnnotation'
IlluminaMethylationManifest-class
                        Class '"IlluminaMethylationManifest"'
MethylSet-class         MethylSet instances
RGChannelSet-class      Class '"RGChannelSet"'
RatioSet-class          RatioSet instances
blockFinder             Finds blocks of methylation differences for
                        Illumina methylation arrays
bumphunter,GenomicRatioSet-method
                        Methods for function 'bumphunter' in Package
                        'minfi'
controlStripPlot        Plot control probe signals.
cpgCollapse             Collapse methylation values of adjacent CpGs
                        into a summary value.
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
estimateCellCounts      Cell Proportion Estimation
fixMethOutliers         Fix methylation outliers
getAnnotation           Accessing annotation for Illumina methylation
                        objects
getMethSignal           Various utilities
getQC                   Estimate sample-specific quality control (QC)
                        for methylation data
getSex                  Estimating sample sex based on methylation data
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
minfiQC                 easy one-step QC of methylation object
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
preprocessFunnorm       Functional normalization for Illumina 450k
                        arrays
preprocessIllumina      Perform preprocessing as Genome Studio.
preprocessNoob          The Noob background correction for 450k arrays.
preprocessQuantile      Stratified quantile normalization for an
                        Illumina methylation array.
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
ratioConvert-methods    Converting methylation signals to ratios (Beta
                        or M-values)
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
