ExomeDepth (version 1.0.7)

viterbi.hmm: Computes the Viterbi path for a hidden markov model

Description

Estimates the most likely path for a hidden Markov Chain using the maximum likelihood Viterbi algorithm.

Usage

viterbi.hmm(transitions, loglikelihood, positions, expected.CNV.length)

Arguments

transitions

Transition matrix

loglikelihood

numeric matrix containing the loglikelihood of the data under the possible states

positions

Positions of the exons

expected.CNV.length

Expected length of CNV calls, which has an impact on the transition matrix between CNV states.

Value

• comp1
  Description of 'comp1'
• comp2
  Description of 'comp2'

Details

Standard forward-backward Viterbi algorithm using a precomputed matrix of likelihoods.