PCASamples              Principal Components Analysis of Methylation
                        data
adjustMethylC           Adjust measured 5mC levels using 5hmC levels
assocComp               Associate principal components with sample
                        annotations
bedgraph                Get bedgraph from methylRaw, methylRawList and
                        methylDiff objects
calculateDiffMeth       Calculate differential methylation statistics
calculateDiffMethDSS    calculate Differential Methylation with DSS
clusterSamples          Hierarchical Clustering using methylation data
                        The function clusters samples using 'hclust'
                        function and various distance metrics derived
                        from percent methylation per base or per region
                        for each sample.
dataSim                 Simulate DNA methylation data
diffMethPerChr          Get and plot the number of hyper/hypo
                        methylated regions/bases per chromosome
extract                 extract parts of
                        methylRaw,methylRawDB,methylBase,methylBaseDB
                        and methylDiff data
filterByCoverage        Filter methylRaw, methylRawDB, methylRawList
                        and methylRawListDB object based on read
                        coverage
getAssembly             get assembly of the genome
getContext              get the context of methylation
getCorrelation          get correlation between samples in methylBase
                        or methylBaseDB object
getCoverageStats        get coverage stats from methylRaw object
getDBPath               Get path to database of the methylDB objects
getData                 get the data slot from the methylKit objects
getMethylDiff           get differentially methylated regions/bases
                        based on cutoffs
getMethylationStats     get Methylation stats from methylRaw or
                        methylRawDB object
getSampleID             Get or Set Sample-IDs of the methylKit objects
getTreatment            Get or Set treatment vector of methylKit object
joinSegmentNeighbours   Join directly neighbouring segments produced by
                        methSeg
makeMethylDB            coerce methylKit objects from memory to flat
                        file database objects
methRead                read file(s) to methylRaw or methylRawList
                        objects
methSeg                 Segment methylation or differential methylation
                        profile
methSeg2bed             Export segments to BED files
methylBase-class        An S4 class for methylation events sampled in
                        multiple experiments
methylBase.obj          Example methylBase object.
methylBaseDB-class      An S4 class for storing methylation events
                        sampled in multiple experiments as flat file
                        database
methylDiff-class        An S4 class that holds differential methylation
                        information
methylDiff.obj          Example methylKit objects.
methylDiffDB-class      An S4 class that holds differential methylation
                        information as flat file database
methylKit-defunct       Deprecated/Defunct functions
methylRaw-class         An S4 class for holding raw methylation data
                        from an alignment pipeline.
methylRawDB-class       An S4 class for storing raw methylation data as
                        flat file database.
methylRawList-class     An S4 class for holding a list of methylRaw
                        objects.
methylRawList.obj       Example methylRawList object.
methylRawListDB-class   An S4 class for holding a list of methylRawDB
                        objects.
normalizeCoverage       normalize read coverage between samples
percMethylation         get percent methylation scores from methylBase
                        or methylBaseDB object
pool                    Pool replicates within groups to a single
                        sample per group
processBismarkAln       Get methylation percentage from sorted Bismark
                        alignments
readMethylDB            load tabix file with header to methylDB
reconstruct             Reconstruct methylBase or methylBaseDB object
                        based on a new methylation percentage matrix
regionCounts            Get regional counts for given GRanges or
                        GRangesList object
removeComp              Remove principal components from a methylBase
                        object
reorganize              Reorganize methylKit objects by creating new
                        objects from subset of samples
select                  selects rows from of methylKit objects
selectByOverlap         selects records of methylDB objects lying
                        inside a GRanges range
show,methylBase-method
                        show method for methylKit classes
tileMethylCounts        Get methylated/unmethylated base counts for
                        tilling windows
unite                   unite methylRawList to a single table
updateMethObject        update methylKit objects The method updates
                        object from earlier versions (<v0.9.1) to
                        latest object.
