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. |