BSdata-class            Class "BSdata"
BSdataSet-class         Class "BSdataSet"
BSprepare               Preparing tabular data to be used to feed a
                        BSdata object
GEcollection-class      Class "GEcollection"
GElist-class            Class "GElist"
chiCombP                Fisher's method implementation
consolidateDMRs         Consolidating Differentially Methylated Regions
                        (DMRs)
extractBinGRanges       Extract genomic ranges for a given bin
findDMR                 Identifying Differentially Methylated Regions
                        (DMRs)
findPMDs                Identifying Partially Methylated Domains (PMDs)
getCpos                 Get genomic Cxx positons for a series of
                        genomic regions
getCposDensity          Determines the density of genomic Cxx positions
                        for a series of genomic regions
mCsmoothing             Smoothing and plotting methylation data
mapBSdata2GRanges       Retrieve mC calls for a GRanges set of genomic
                        regions given a BSdata object for a sample
meth.call               Function to read methylation calls
methstats               Exploratory statistics of samples in BSdataSet
                        object
methylPipe-package      Analysis of base-pair resolution DNA
                        methylation data.
plotMeth                Plot DNA methylation together with other omics,
                        or annotation data for a genomic region
pool.reads              Function to pool reads of replicates
process.hmc             Processing hmC information from the MLML output
profileDNAmetBin        Profile DNA methylation data for a set of
                        genomic regions
splitChrs               Partitioning genome in chunks, for parallel
                        computation
tabixdata2GR            Convert the list returned by the function
                        scanTabix into a GRanges
