Man pages for STAN
The Genomic STate ANnotation Package

bdHMMCreate a bdHMM object
bdHMM-classThis class is a generic container for bidirectional Hidden...
binarizeDataBinarize Sequencing data with the default ChromHMM...
c2optimizeOptimize transitions
call_dpoilogCalculate density of the Poisson-Log-Normal distribution.
data2GvizConvert data for plotting with Gviz
DimNamesGet dimNames of a (bd)HMM
DirScoreGet directionality score of a bdHMM
EmissionGet Emission functions of a (bd)HMM
EmissionParamsGet Emission parameters of a (bd)HMM.
exampleThe data for the bdHMM example in the vignette and examples...
fitBdClustFit a bidirectional Clustering
fitHMMFit a Hidden Markov Model
flagsPre-computed flag sequence for the 'example' data.
getAvgSignalCompute average signal in state segmentation
getLogLikCalculate log likelihood state distribution.
getPosteriorCalculate posterior state distribution.
getSizeFactorsCompute size factors
getViterbiCalculate the most likely state path
HMMCreate a HMM object
HMM-classThis class is a generic container for Hidden Markov Models.
HMMEmissionCreate a HMMEmission object
HMMEmission-classThis class is a generic container for different emission...
initBdClustInitialization of bidirectional Clustering
initBdHMMInitialization of bidirectional hidden Markov models
initHMMInitialization of hidden Markov models
InitProbGet initial state probabilities of a (bd)HMM
LogLikGet stateNames of a (bd)HMM
observationsObservation sequence for the 'example' data.
pilot.hg19Genomic positions of processed signal for the Roadmap...
runningMeanSmooth data with running mean
STAN-packageThe genomic STate ANnotation package
StateNamesGet stateNames of a (bd)HMM
sub-bdHMM-ANY-ANY-ANY-methodextract parts of bdHMM
sub-HMM-ANY-ANY-ANY-methodextract parts of HMM
trainRegionsTraining regions for the Roadmap Epigenomics data set. Three...
TransitionsGet transitions of a (bd)HMM
ucscGenesUCSC gene annotation for the Roadmap Epigenomics data set.
viterbi2GRangesConvert the viterbi path to a GRanges object
viterbi2GvizConvert state segmentation for plotting with Gviz
yeastTF_databychrom_exProcessed ChIP-on-chip data for yeast TF example
yeastTF_SGDGenesSGD annotation for the yeast TF example
STAN documentation built on Nov. 8, 2020, 11:11 p.m.