HmmParam: Constructor for HmmParam class

In VanillaICE: A Hidden Markov Model for high throughput genotyping arrays

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()

VanillaICE documentation built on Nov. 8, 2020, 7:33 p.m.