getViterbi: Calculate the most likely state path

In STAN: The Genomic STate ANnotation Package

Description

Given a Hidden Markov Model, the function calculates the most likely state path (viterbi) for one or more observation sequence.

Usage

getViterbi(hmm, obs=list(), NAtol=5, emissionProbs=list(), verbose=FALSE, sizeFactors=matrix(1, nrow=length(obs), ncol=ncol(obs[[1]])))

Arguments

hmm	The initial Hidden Markov Model.
obs	The observations. A list of one or more entries containing the observation matrix (numeric) for the samples (e.g. chromosomes).
NAtol	Successive positions having NAs longer than this threshold are masked in the viterbi path.
emissionProbs	List of precalculated emission probabilities of emission function is of type 'null'.
verbose	logical for printing algorithm status or not.
sizeFactors	Library size factors for Emissions PoissonLogNormal or NegativeBinomial as a length(obs) x ncol(obs[[1]]) matrix.

Value

A list containint the vterbi paths.

Examples

data(example)
hmm_ex = initHMM(observations, nStates=3, method="Gaussian") 
hmm_fitted = fitHMM(observations, hmm_ex)
viterbi = getViterbi(hmm_fitted, observations)

STAN documentation built on Nov. 8, 2020, 11:11 p.m.