HmmParam: Constructor for HmmParam class

Description Usage Arguments Examples

Description

Contains emission probabilities, parameters for emission probabilities, and transition probabilities required for computing the most likely state path via the Viterbi algorithm

Usage

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HmmParam(emission = matrix(0, 0, 0), emission_param = EmissionParam(),
  transition = rep(0.99, nrow(emission)),
  chromosome = character(nrow(emission)), loglik = LogLik(),
  viterbi = Viterbi(), compute_posteriors = TRUE, verbose = FALSE)

## S4 method for signature 'HmmParam'
show(object)

## S4 method for signature 'HmmParam'
nrow(x)

## S4 method for signature 'HmmParam'
ncol(x)

Arguments

emission

A matrix of emission probabilities

emission_param

an object of class EmissionParam

transition

vector of transition probabilities whose length is N-1, where N is the number of markers. User should provide the probability that the state at marker j is the same as the state at marker j-1. It is assumed that the probability of transitioning to state_j from state_j-1 is the same for all states != state_j-1.

chromosome

character vector

loglik

an object of class LogLik

viterbi

an object of class Viterbi

compute_posteriors

logical

verbose

logical

object

a HmmParam object

x

a HmmParam object

Examples

1


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