callDML                 Function to detect differntially methylated
                        loci (DML) from bisulfite sequencing (BS-seq)
                        data.
callDMR                 Function to detect differntially methylated
                        regions (DMR) from bisulfite sequencing
                        (BS-seq) data.
design                  Experimental design for the example RRBS
                        dataset
dispersion              Acessor functions for the 'dispersion' slot in
                        a SeqCountData object.
DMLfit.multiFactor      Fit a linear model for BS-seq data from general
                        experimental design
DMLtest                 Function to perform statistical test of
                        differntially methylated loci (DML) for two
                        group comparisons of bisulfite sequencing
                        (BS-seq) data.
DMLtest.multiFactor     Perform statistical test for BS-seq data from
                        general experimental design
DSS-package             Dispersion shrinkage for sequencing data
DSS.DE                  Perform RNA-seq differential expression
                        analysis in two-group comparison
estDispersion           Estimate and shrink tag-specific dipsersions
estNormFactors          Estimate normalization factors
makeBSseqData           Create an object of BSseq class from several
                        data frames.
normalizationFactor     Accessor functions for the
                        'normalizationFactor' slot in a SeqCountData
                        object.
RRBS                    An example dataset for multiple factor design
SeqCountSet-class       Class '"SeqCountSet"' - container for count
                        data from sequencing experiment
seqData                 A simulated 'SeqCountData' object.
showOneDMR              Visualze the count data for one DMR
waldTest                Perform gene-wise Wald test for two group
                        comparisons for sequencing count data.
