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 (