Methods for Penetrance Estimation in Family-Based Studies
Function to return absolute values
Apply Burn-In
Apply Thinning
Default Baseline Data
Calculate Weibull Parameters
Calculate Baseline Risk
Calculate Empirical Age Density
Calculate Age-Specific Non-Carrier Penetrance
Combine Chains for Non-Sex-Specific Estimation
Combine Chains Function to combine the posterior samples from the mult...
Default Distribution Data
Draw Ages Using the Inverse CDF Method from the baseline data
Draw Ages Using the Inverse CDF Method from Empirical Density
Generate Posterior Density Plots
Generate Summary for Non-Sex-Specific Estimation
Generate Summary
Impute Missing Ages in Family-Based Data
Initialize Age Imputation
Impute Ages for Unaffected Individuals
Likelihood Calculation without Sex Differentiation
Penetrance Function
Make Priors
Execution of a Single Chain in Metropolis-Hastings for Cancer Risk Est...
Calculate Log Likelihood without Sex Differentiation
Calculate Log Likelihood using clipp Package
penetrance: A Package for Penetrance Estimation
Plot Autocorrelation for Multiple MCMC Chains (Posterior Samples)
Plot Log-Likelihood for Multiple MCMC Chains
Plot Weibull Probability Density Function with Credible Intervals
Plot Weibull Distribution with Credible Intervals
Plot MCMC Trace Plots
Print MCMC Rejection Rates
Default Prior Parameters
Default Risk Proportions
Transform Data Frame
Validate Weibull Parameters
Implements statistical methods for estimating disease penetrance in family-based studies. Penetrance refers to the probability of disease§ manifestation in individuals carrying specific genetic variants. The package provides tools for age-specific penetrance estimation, handling missing data, and accounting for ascertainment bias in family studies. Cite as: Kubista, N., Braun, D. & Parmigiani, G. (2024) <doi:10.48550/arXiv.2411.18816>.