summary.BeviMed_m: Summarise a 'BeviMed_m' object
In BeviMed: Bayesian Evaluation of Variant Involvement in Mendelian Disease

summary.BeviMed_m

R Documentation

Summarise a `BeviMed_m` object

Create a summary of inference conditional on mode of inheritance.

## S3 method for class 'BeviMed_m'
summary(object, confidence = 0.95, simulations = 1000, ...)

`object`	Object of class `BeviMed_m`. See function `bevimed_m`.
`confidence`	Numeric value of statistical confidence with which returning interval should contain the true value.
`simulations`	Integer value of number of simulations to use in estimation of the confidence interval.
`...`	Unused arguments.

Returns a BeviMed_m_summary object, which is a list containing elements:

‘gamma1_evidence’: the log evidence under model gamma = 1,
‘gamma1_evidence_confidence_interval’: a confidence interval for the log evidence under model gamma = 1,
‘conditional_prob_pathogenic’: vector of marginal probabilities of pathogenicity for individual variants,
‘expected_explained’: the expected number of cases with a pathogenic configuration of alleles,
‘explaining_variants’: the expected number of variants present for which cases harbour a rare allele,
‘number_of_posterior_samples’: the number of samples from the posterior distribution of the model parameters which upon which the summary is based,
‘omega_estimated’: logical value indicating whether the parameter omega was estimated,
‘omega’: the posterior mean of omega,
‘omega_acceptance_rate’: if omega was estimated, the rate of acceptance of proposed omega values in the Metropolis-Hastings sampling routine,
‘phi_estimated’: logical value indicating whether the parameter phi was estimated,
‘tau’: the posterior mean of tau,
‘pi’: the posterior mean of pi,
‘phi’: the posterior mean of phi,
‘phi_acceptance_rate’: if phi was estimated, the rate of acceptance of proposed phi values in the Metropolis-Hastings sampling routine,
'N': number of samples in the analysis,
'k': number of variants in the analysis,
‘variant_counts’: list of counts of each variant for cases and controls,
‘temperatures’: numeric vector of temperatures used as temperatures for tempered MCMC chains

Object of class BeviMed_m_summary.