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 |