Description Usage Arguments Examples

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
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)
``` |

`emission` |
A matrix of emission probabilities |

`emission_param` |
an object of class |

`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 |

`viterbi` |
an object of class |

`compute_posteriors` |
logical |

`verbose` |
logical |

`object` |
a |

`x` |
a |

1 | ```
HmmParam()
``` |

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