viterbi {VanillaICE}R Documentation

viterbi algorithm

Description

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

Usage

viterbi(initialStateProbs, emission, tau, arm, tau.scale, verbose = TRUE, returnLikelihood = FALSE)

Arguments

initialStateProbs initial state probabilities (log scale)
emission matrix of log emission probabilities (one sample is a matrix)
tau transition probabilities (original scale)
arm numeric or character string indicating chromosomal arm
tau.scale matrix to scale the probability of transitioning between states.
verbose Logical
returnLikelihood whether to return the 'loglikelihood'

Details

The Viterbi algorithm is fit independently to each chromosomal arm if arm is specified.

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. If missing, tau.scale is 1 (no scaling)

returnLikelihood is experimental

Value

matrix predicted states

Author(s)

R. Scharpf


[Package VanillaICE version 1.4.0 Index]