addOffsets              Add offsets to epigraHMMDataSet
callPatterns            Extract posterior probabilities (or
                        combinatorial patterns) associated with
                        differential regions
callPeaks               Summarize peak calls and optionally create a
                        BED 6+3 file in broadPeak format for
                        visualization
cleanCounts             Remove effects from covariates of interest
controlEM               Control parameters for the EM algorithm from
                        epigraHMM
epigraHMM               Perform peak calling of epigenomic data sets
epigraHMMDataSetFromBam
                        Create a epigraHMMDataSet from a set of BAM
                        files
epigraHMMDataSetFromMatrix
                        Create a epigraHMMDataSet from matrices of
                        counts
estimateTransitionProb
                        Estimate transition probability from a sequence
                        of integers
expStep                 E-step of HMM (forward-backward probability +
                        posterior probability calculation)
helas3                  ENCODE ChIP-seq broad data from Helas3 cell
                        line
info                    Get information about peak calling results
initializer             Initializer of epigraHMM
maxStepProb             M-step (maximization w.r.t. initial and
                        transition probabilities)
normalizeCounts         Normalize counts
plotCounts              Create a plot with the results from epigraHMM
plotPatterns            Create a plot of differerential patterns
                        posterior probabilities from epigraHMM
segmentGenome           Segmentation of a genome in non-overlapping
                        windows
simulateMarkovChain     Simulates a Markov Chain of length 'n' given a
                        matrix of transition probabilities P
