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'
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
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
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.
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)
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
subsetByLoci            Subset an RGChannelset by CpG loci.
