# The Genomic STate ANnotation Package

## Documentation for package ‘STAN’ version 2.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

STAN-package | The genomic STate ANnotation package
.bdHMM | This class is a generic container for bidirectional Hidden Markov Models.
.HMM | This class is a generic container for Hidden Markov Models.
.HMMEmission | This class is a generic container for different emission functions of Hidden Markov Models.
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
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.
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
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.
initBdClust | Initialization of bidirectional Clustering
initBdHMM | Initialization of bidirectional hidden Markov models
initHMM | Initialization of hidden Markov models
InitProb | Get initial state probabilities of a (bd)HMM
LogLik | Get stateNames of a (bd)HMM
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
StateNames | Get stateNames of a (bd)HMM
trainRegions | Training regions for the Roadmap Epigenomics data set. Three ENCODE pilot regions with data from two cell lines.
Transitions | Get transitions of a (bd)HMM
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_databychrom_ex | Processed ChIP-on-chip data for yeast TF example
yeastTF_SGDGenes | SGD annotation for the yeast TF example
[-method | extract parts of HMM
[-method | extract parts of bdHMM