blockFinder             Finds blocks of methylation differences for
                        Illumina methylation arrays
bumphunter,GenomicRatioSet-method
                        Methods for function 'bumphunter' in Package
                        'minfi'
combineArrays           A method for combining different types of
                        methylation arrays into a virtual array.
compartments            Estimates A/B compartments from Illumina
                        methylation arrays
controlStripPlot        Plot control probe signals.
convertArray            A method for converting a type of methylation
                        arrays into a virtual array of another type.
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
gaphunter               Find gap signals in 450k data
GenomicMethylSet-class
                        GenomicMethylSet instances
GenomicRatioSet-class   GenomicRatioSet instances
getAnnotation           Accessing annotation for Illumina methylation
                        objects
getGenomicRatioSetFromGEO
                        Reading Illumina methylation array data from
                        GEO.
getMethSignal           Various utilities
getQC                   Estimate sample-specific quality control (QC)
                        for methylation data
getSex                  Estimating sample sex based on methylation data
IlluminaMethylationAnnotation-class
                        Class 'IlluminaMethylationAnnotation'
IlluminaMethylationManifest-class
                        Class '"IlluminaMethylationManifest"'
logit2                  logit in base 2.
makeGenomicRatioSetFromMatrix
                        Make a GenomicRatioSet from a matrix
mapToGenome-methods     Mapping methylation data to the genome
mdsPlot                 Multi-dimensional scaling plots giving an
                        overview of similarities and differences
                        between samples.
MethylSet-class         MethylSet instances
minfi-defunct           Defunct functions in package 'minfi'
minfi-deprecated        Deprecated functions in package 'minfi'
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/ssNoob preprocessing method for
                        Infinium methylation microarrays.
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)
RatioSet-class          RatioSet instances
read.metharray          Parsing IDAT files from Illumina methylation
                        arrays.
read.metharray.exp      Reads an entire metharray experiment using a
                        sample sheet
read.metharray.sheet    Reading an Illumina methylation sample sheet
readGEORawFile          Read in Unmethylated and Methylated signals
                        from a GEO raw file.
readTCGA                Read in tab deliminited file in the TCGA format
RGChannelSet-class      Class '"RGChannelSet"'
subsetByLoci            Subset an RGChannelset by CpG loci.
