DimNames                Get dimNames of a (bd)HMM
DirScore                Get directionality score of a bdHMM
Emission                Get Emission functions of a (bd)HMM
EmissionParams          Get Emission parameters of a (bd)HMM.
HMM                     Create a HMM object
HMM-class               This class is a generic container for Hidden
                        Markov Models.
HMMEmission             Create a HMMEmission object
HMMEmission-class       This class is a generic container for different
                        emission functions of Hidden Markov Models.
InitProb                Get initial state probabilities of a (bd)HMM
LogLik                  Get stateNames of a (bd)HMM
STAN-package            The genomic STate ANnotation package
StateNames              Get stateNames of a (bd)HMM
Transitions             Get transitions of a (bd)HMM
[,HMM,ANY,ANY,ANY-method
                        extract parts of HMM
[,bdHMM,ANY,ANY,ANY-method
                        extract parts of bdHMM
bdHMM                   Create a bdHMM object
bdHMM-class             This class is a generic container for
                        bidirectional Hidden Markov Models.
binarizeData            Binarize Sequencing data with the default
                        ChromHMM binarization
c2optimize              Optimize transitions
call_dpoilog            Calculate density of the Poisson-Log-Normal
                        distribution.
data2Gviz               Convert data for plotting with Gviz
example                 The data for the bdHMM example in the vignette
                        and examples in the manual
fitBdClust              Fit a bidirectional Clustering
fitHMM                  Fit a Hidden Markov Model
flags                   Pre-computed flag sequence for the 'example'
                        data.
getAvgSignal            Compute average signal in state segmentation
getLogLik               Calculate log likelihood state distribution.
getPosterior            Calculate posterior state distribution.
getSizeFactors          Compute size factors
getViterbi              Calculate the most likely state path
initBdClust             Initialization of bidirectional Clustering
initBdHMM               Initialization of bidirectional hidden Markov
                        models
initHMM                 Initialization of hidden Markov models
observations            Observation sequence for the 'example' data.
pilot.hg19              Genomic positions of processed signal for the
                        Roadmap Epigenomics data set. Regions from the
                        ENCODE pilot phase.
runningMean             Smooth data with running mean
trainRegions            Training regions for the Roadmap Epigenomics
                        data set. Three ENCODE pilot regions with data
                        from two cell lines.
ucscGenes               UCSC gene annotation for the Roadmap
                        Epigenomics data set.
viterbi2GRanges         Convert the viterbi path to a GRanges object
viterbi2Gviz            Convert state segmentation for plotting with
                        Gviz
yeastTF_SGDGenes        SGD annotation for the yeast TF example
yeastTF_databychrom_ex
                        Processed ChIP-on-chip data for yeast TF
                        example
