Man pages for BeviMed
Bayesian Evaluation of Variant Involvement in Mendelian Disease

bevimedBayesian Evaluation of Variant Involvement in Mendelian...
bevimed_mPerform inference under model gamma = 1 conditional on mode...
BeviMed-packageBayesian Evaluation of Variant Involvement in Mendelian...
bevimed_polytomousModel selection for multiple association models
call_cppR interface to BeviMed c++ MCMC procedure
CI_gamma1_evidenceEstimate confidence interval for estimated marginal...
conditional_prob_pathogenicCalculate probability of pathogencity for variants...
exact_evidenceCalculate exact evidence for model gamma = 1
expected_explainedCalculate expected number of explained cases
explaining_variantsCalculate expected number of pathogenic variants in cases
extract_conditional_prob_pathogenicExtract probability of pathogenicity for variant conditional...
extract_expected_explainedExtract expected number of explained cases
extract_explaining_variantsExtract expected number of pathogenic variants in cases
extract_gamma1_evidenceExtract evidence for model gamma = 1
extract_prob_associationExtract the posterior probability of association
extract_prob_pathogenicExtract variant marginal probabilities of pathogenicity
gamma0_evidenceCalculate marginal probability of observed case-control...
gamma1_evidenceCalculate evidence under model gamma = 1
log_BFCalculate log Bayes factor between an association model with...
lower_bound_gamma1_evidenceCalculate log lower bound for marginal probability under...
print.BeviMedPrint readable summary of 'BeviMed' object
print.BeviMed_mPrint 'BeviMed_m' object
print.BeviMed_summaryPrint readable summary of 'BeviMed_summary' object.
prob_associationCalculate probability of association
prob_association_mCalculate probability of association for one mode of...
prob_pathogenicCalculate variant marginal probabilities of pathogencity
region_association_evidenceCalculate evidence of under pathogenic locus model
stack_BeviMedsConcatenate objects of class 'BeviMed_raw'
stop_chainApply the MCMC algorithm in blocks until conditions are met
subset_variantsRemove variants with no data for pathogenicity
summary.BeviMedSummarise a 'BeviMed' object
summary.BeviMed_mSummarise a 'BeviMed_m' object
sum_ML_over_PPCalculate marginal likelihood from power posteriors output
tune_proposal_sdsTune proposal standard deviation for MH sampled parameters
tune_temperaturesTune temperatures
BeviMed documentation built on Aug. 21, 2017, 5:05 p.m.