Computes the Bayes Factor in favour of a CNV defined by...

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

1 | ```
viterbi.hmm(transitions, loglikelihood, positions, expected.CNV.length)
``` |

`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. |

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

`comp1 ` |
Description of 'comp1' |

`comp2 ` |
Description of 'comp2' |

Vincent Plagnol

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