BS.chr22                Whole-genome bisulfite sequencing for
                        chromosome 22 from Lister et al.
BSmooth                 BSmooth, smoothing bisulfite sequence data
BSmooth.tstat           Compute t-statistics based on smoothed
                        whole-genome bisulfite sequencing data.
BSseq                   The constructor function for BSseq objects.
BSseq-class             Class BSseq
BSseqStat-class         Class BSseqStat
BSseqTstat-class        Class BSseqTstat
FWGRanges-class         Classes FWIRanges and FWGRanges
data.frame2GRanges      Converts a data frame to a GRanges.
dmrFinder               Finds differentially methylated regions for
                        whole genome bisulfite sequencing data.
findLoci                Find methylation loci in a genome
fisherTests             Compute Fisher-tests for a BSseq object
getCoverage             Obtain coverage for BSseq objects.
getMeth                 Obtain methylation estimates for BSseq objects.
getStats                Obtain statistics from a BSseqTstat object
hasGRanges-class        Class hasGRanges
plotRegion              Plotting BSmooth methylation estimates
poissonGoodnessOfFit    Binomial and poisson goodness of fit statistics
                        for BSSeq objects
read.bismark            Parsing output from the Bismark alignment
                        suite.
read.bsmooth            Parsing output from the BSmooth alignment suite
read.umtab              Parsing UM tab files (legacy output) containing
                        output from the BSmooth aligner.
