hmm-class: Class "hmm"

In humburg/tileHMM: Hidden Markov Models for ChIP-on-Chip Analysis

Description

Virtual base class for HMMs.

Objects from the Class

Do not create objects of this class directly. Instead use objects of derived classes like "contHMM".

Slots

transition.matrix:

Object of class "matrix", storing the transition probabilities of the Markov chain.

emission:

Object of class "list" containing objects of class "dist" to represent emission distributions for each state.

init:

Object of class "numeric". The initial state distribution of the Markov chain.

Methods

baumWelch

signature(hmm = "hmm", obs = "list"): Baum-Welch algorithm to estimate model parameters.

viterbiTraining

signature(hmm = "hmm", obs = "list"): Viterbi training to estimate model parameters.

viterbi

signature(hmm = "hmm"): Viterbi algorithm to calculate most likely state sequence.

backward

signature(hmm = "hmm"): Computing of backward variables.

forward

signature(hmm = "hmm"): Computing of forward variables.

states

signature(hmm = "hmm"): Returns state names.

show

signature(object = "hmm"): Print summary of hmm object.

Author(s)

Peter Humburg

See Also

contHMM, baumWelch, viterbiTraining, viterbi, forward, backward, states

Examples

showClass("hmm")

humburg/tileHMM documentation built on May 17, 2019, 9:13 p.m.