Knockoffs for Hidden Markov Models and Genetic Data

assemble_pEmit | Compute the genotype emission distributions based on the... |

assemble_pEmit_phased | Compute the haplotype emission distributions based on the... |

assemble_pInit | Compute the genotype initial distributions based on the... |

assemble_pInit_phased | Compute the haplotype initial distributions based on the... |

assemble_Q | Compute the genotype transition matrices based on the... |

compute_Q1 | Compute the haplotype transition matrices based on the... |

GroupGenotypes_wrapper | Wrapper for GroupGenotypes |

GroupHaplotypes_wrapper | Wrapper for GroupHaplotypes |

knockoffDMC | Group knockoffs of discrete Markov chains |

knockoffDMC_wrapper | Wrapper for DMC group knockoffs |

knockoffGenotypes | Group-knockoffs of unphased genotypes |

knockoffHaplotypes | Group-knockoffs of phased haplotypes |

knockoffHMM | Group knockoffs of hidden Markov models |

knockoffHMM_wrapper | Wrapper for HMM group knockoffs |

loadEMParameters | Read the files produced by fastPHASE |

loadHMM | Load HMM parameters fitted by fastPHASE |

rand_weighted | Random sampling from discrete distribution |

runFastPhase | Fit an HMM to genetic data using fastPHASE |

sampleDMC | Sample discrete Markov chains |

sampleHMM | Sample hidden Markov models |

writeXtoInp | Convert genotypes X into the fastPHASE input format |

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