viterbi {VanillaICE} | R Documentation

## viterbi algorithm

### Description

The Viterbi algorithm for computing the most likely state sequence given a model

### Usage

    viterbi(beta, pi, tau, states, arm, tau.scale)

### Arguments

`beta` | emission probabilities (log scale)
`pi` | initial state probabilities (log scale)
`tau` | transition probabilities (log scale)
`states` | character string of hidden states
`arm` | character string of chromosomal arm
`tau.scale` | scales the probability of transitioning between an altered state to a normal state relative to the probability of transitioning between two altered states.

### Details

The Viterbi algorithm is fit independently to each chromosomal arm.

Argument `tau.scale` is a matrix that scales the probability of transitioning from an altered state to a normal state to the probability of transitioning between two altered states.

When initializing an object of class `HmmParameter`, the default is to make the probability of transitioning from an altered state to a normal state twice the probability of transitioning between two altered states. Further flexibility could be obtained by replacing the tau.scale matrix in an instance of the `HmmParameter` class with your own matrix. The dimension of this matrix must be S x S, where S is the number of hidden states.

### Value

vector of integers

### Author(s)

R. Scharpf

[Package VanillaICE version 1.2.0 Index]