Description Usage Arguments Value See Also Examples
The function calculates log likelihood for one or more observation sequence.
1 
hmm 
The Hidden Markov Model. 
obs 
The observations. A list of one or more entries containing the observation matrix ( 
emissionProbs 
List of precalculated emission probabilities of emission function is of type 'null'. 
dirFlags 
The flag sequence is needed when a bdHMM is fitted on undirected data (e.g.) ChIP only. It is a 
verbose 

nCores 
Number of cores to use for computations. 
sizeFactors 
Library size factors for Emissions PoissonLogNormal or NegativeBinomial as a length(obs) x ncol(obs[[1]]) matrix. 
The log likelihood of the observations sequences, given the model.
1 2 3 4 5  data(example)
hmm_ex = initHMM(observations, nStates=3, method="Gaussian")
hmm_fitted = fitHMM(observations, hmm_ex)
loglik = getLogLik(hmm_fitted, observations)
loglik

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