Bayesian Evaluation of Variant Involvement in Mendelian Disease

bevimed | Bayesian Evaluation of Variant Involvement in Mendelian... |

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

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

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... |

conditional_prob_pathogenic | Calculate probability of pathogencity for variants... |

exact_evidence | Calculate exact evidence for model gamma = 1 |

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... |

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... |

gamma1_evidence | Calculate evidence under model gamma = 1 |

log_BF | Calculate log Bayes factor between an association model with... |

lower_bound_gamma1_evidence | Calculate log lower bound for marginal probability under... |

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... |

prob_pathogenic | Calculate variant marginal probabilities of pathogencity |

region_association_evidence | Calculate evidence of under pathogenic locus model |

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 |

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