HmmParam {VanillaICE} | R Documentation

## Constructor for HmmParam class

### Description

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

### Usage

    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

    HmmParam()

[Package VanillaICE version 1.48.0 Index]