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`

.

### See Also

*BeviMed*version 5.10 Index]