Bayesian Evaluation of Variant Involvement in Mendelian Disorders


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Documentation for package ‘BeviMed’ version 2.2

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ccvt-package A short title line describing what the package does
bevimed Perform inference under model gamma = 1
call_cpp R interface to BeviMed c++ MCMC procedure
ccvt A short title line describing what the package does
CI_gamma1_evidence Estimate confidence interval for estimated marginal likelihood by simulation
conditional_prob_pathogenic Calculate probability of pathogencity for variants in region given an association between case label and the region
exact_evidence Calculate exact evidence for model gamma=1
gamma0_evidence Calculate marginal probability of observed case-control status y under model gamma = 0
gamma1_evidence Calculate marginal probability of observed case-control status under model gamma = 1
gamma1_prob Calculate probability of an association
log_BF Calculate log Bayes factor between models gamma=1 and gamma=0 given the data
lower_bound_gamma1_evidence Calculate log lower bound for marginal probability of observations under model gamma = 1 by summing likelihood over pathogenic variant (Z) configurations, or probabilities that individual variants are pathogenic.
print.BeviMed Print readable summary of 'BeviMed' object.
print.BeviMed_summary Print readable summary of 'BeviMed_summary' object.
prob_association Calculate probability of an association between presence/absence of local genotype configuration and case-control label
prob_pathogenic Calculate probability of pathogencity for variants in region given a prior probability of association between case label and the region
region_association_evidence Calculate marginal probability of observed genotypes under 'pathogenic region' model
stack_BeviMeds Concatenate objects of class 'BeviMed'
stop_chain Apply the MCMC algorithm in blocks until conditions are met
summary.BeviMed Create summary of 'BeviMed' classed-object
sum_ML_over_PP Calculate the Marginal Likelihood by summation over power posterior likelihood exptectances
tune_proposal_sds Tune the proposal standard deviations for the Metropolis-Hastings updates of either phi or omega
tune_temperatures Tune temperatures using interval bisection to minimimise Kullback-Liebler divergence between adjacent power posteriors