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

Description Usage Arguments Details Value Author(s)

Description

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

Usage

1
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.

Details

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

Value

comp1

Description of 'comp1'

comp2

Description of 'comp2'

Author(s)

Vincent Plagnol



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