Knockoffs for Hidden Markov Models and Genomic Data

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

assemble_pInit | Compute the genotype 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... |

knockoffDMC_wrapper | Wrapper for DMC knockoffs |

knockoffHMM_wrapper | Wrapper for HMM knockoffs |

loadEMParameters | Read the files produced by fastPhase |

rand_weighted | Random sampling from discrete distribution |

SNPknock.fp.loadFit | Load the parameter estimates obtained by fastPhase and... |

SNPknock.fp.runFastPhase | Calls fastPhase to fit an HMM to genotype data. |

SNPknock.fp.writeX | Convert a genetic matrix X into the fastPhase input format. |

SNPknock.knockoffDMC | Sample knockoff copies of a discrete Markov chain. |

SNPknock.knockoffHMM | Sample knockoff copies of a hidden Markov model. |

SNPknock.models.sampleDMC | Sample discrete Markov chains. |

SNPknock.models.sampleHMM | Sample hidden Markov models. |

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