| summary.BeviMed_m {BeviMed} | R Documentation |
Summarise a BeviMed_m object
Description
Create a summary of inference conditional on mode of inheritance.
Usage
## S3 method for class 'BeviMed_m'
summary(object, confidence = 0.95, simulations = 1000, ...)
Arguments
object |
Object of class |
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. |
Details
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,
‘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
Value
Object of class BeviMed_m_summary.