BeviMed-package         Bayesian Evaluation of Variant Involvement in
                        Mendelian Disease
CI_gamma1_evidence      Estimate confidence interval for estimated
                        marginal likelihood
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
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
sum_ML_over_PP          Calculate marginal likelihood from power
                        posteriors output
summary.BeviMed         Summarise a 'BeviMed' object
summary.BeviMed_m       Summarise a 'BeviMed_m' object
tune_proposal_sds       Tune proposal standard deviation for MH sampled
                        parameters
tune_temperatures       Tune temperatures
