VanillaICE (version 1.34.0)

HmmParam: 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)
"show"(object)
"nrow"(x)
"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()