# Bayesian Evaluation of Variant Involvement in Mendelian Disease

## Documentation for package ‘BeviMed’ version 5.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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