BeviMed-package |
Bayesian Evaluation of Variant Involvement in Mendelian Disease |

BeviMed |
Bayesian Evaluation of Variant Involvement in Mendelian Disease |

bevimed |
Bayesian Evaluation of Variant Involvement in Mendelian Disease |

bevimed_m |
Perform inference under model gamma = 1 conditional on mode of inheritance |

bevimed_polytomous |
Model selection for multiple association models |

call_cpp |
R interface to BeviMed c++ MCMC procedure |

CI_gamma1_evidence |
Estimate confidence interval for estimated marginal likelihood |

conditional_prob_pathogenic |
Calculate probability of pathogencity for variants conditional on mode of inheritance. |

expected_explained |
Calculate expected number of explained cases |

explaining_variants |
Calculate expected number of pathogenic variants in cases |

extract_conditional_prob_pathogenic |
Extract probability of pathogenicity for variant conditional on a given association model |

extract_expected_explained |
Extract expected number of explained cases |

extract_explaining_variants |
Extract expected number of pathogenic variants in cases |

extract_gamma1_evidence |
Extract evidence for model gamma = 1 |

extract_prob_association |
Extract the posterior probability of association |

extract_prob_pathogenic |
Extract variant marginal probabilities of pathogenicity |

gamma0_evidence |
Calculate marginal probability of observed case-control status y under model gamma = 0 |

gamma1_evidence |
Calculate evidence under model gamma = 1 |

log_BF |
Calculate log Bayes factor between an association model with a given mode of inheritance and model gamma = 0 |

print.BeviMed |
Print readable summary of 'BeviMed' object |

print.BeviMed_m |
Print 'BeviMed_m' object |

print.BeviMed_summary |
Print readable summary of 'BeviMed_summary' object. |

prob_association |
Calculate probability of association |

prob_association_m |
Calculate probability of association for one mode of inheritance |

prob_pathogenic |
Calculate variant marginal probabilities of pathogencity |

stack_BeviMeds |
Concatenate objects of class 'BeviMed_raw' |

stop_chain |
Apply the MCMC algorithm in blocks until conditions are met |

subset_variants |
Remove variants with no data for pathogenicity |

summary.BeviMed |
Summarise a 'BeviMed' object |

summary.BeviMed_m |
Summarise a 'BeviMed_m' object |

sum_ML_over_PP |
Calculate marginal likelihood from power posteriors output |

tune_proposal_sds |
Tune proposal standard deviation for MH sampled parameters |

tune_temperatures |
Tune temperatures |