The genomic STate ANnotation package


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Documentation for package ‘STAN’ version 2.2.0

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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
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.
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 This class is a generic container for Hidden Markov Models.
[-method This class is a generic container for bidirectional Hidden Markov Models.
[-method This function subsets an HMM object. Rows are interpreted as states, columns as dimensions of emissions.
[-method This function subsets a bdHMM object. Rows are interpreted as states, columns as dimensions of emissions.