# Methods for Penetrance Estimation in Family-Based Studies

## Documentation for package ‘penetrance’ version 0.1.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

penetrance-package | penetrance: A Package for Penetrance Estimation
absValue | Function to return absolute values
apply_burn_in | Apply Burn-In
apply_thinning | Apply Thinning
baseline_data_default | Default Baseline Data
calculateBaseline | Calculate Baseline Risk
calculateEmpiricalDensity | Calculate Empirical Age Density
calculateNCPen | Calculate Age-Specific Non-Carrier Penetrance
calculate_weibull_parameters | Calculate Weibull Parameters
combine_chains | Combine Chains Function to combine the posterior samples from the multiple chains.
combine_chains_noSex | Combine Chains for Non-Sex-Specific Estimation
distribution_data_default | Default Distribution Data
drawBaseline | Draw Ages Using the Inverse CDF Method from the baseline data
drawEmpirical | Draw Ages Using the Inverse CDF Method from Empirical Density
generate_density_plots | Generate Posterior Density Plots
generate_summary | Generate Summary
generate_summary_noSex | Generate Summary for Non-Sex-Specific Estimation
imputeAges | Impute Missing Ages in Family-Based Data
imputeAgesInit | Initialize Age Imputation
imputeUnaffectedAges | Impute Ages for Unaffected Individuals
lik.fn | Penetrance Function
lik_noSex | Likelihood Calculation without Sex Differentiation
makePriors | Make Priors
mhChain | Execution of a Single Chain in Metropolis-Hastings for Cancer Risk Estimation
mhLogLikelihood_clipp | Calculate Log Likelihood using clipp Package
mhLogLikelihood_clipp_noSex | Calculate Log Likelihood without Sex Differentiation
out_sim | Simulated Output Data
penetrance | penetrance: A Package for Penetrance Estimation
plot_acf | Plot Autocorrelation for Multiple MCMC Chains (Posterior Samples)
plot_loglikelihood | Plot Log-Likelihood for Multiple MCMC Chains
plot_pdf | Plot Weibull Probability Density Function with Credible Intervals
plot_penetrance | Plot Weibull Distribution with Credible Intervals
plot_trace | Plot MCMC Trace Plots
printRejectionRates | Print MCMC Rejection Rates
prior_params_default | Default Prior Parameters
risk_proportion_default | Default Risk Proportions
simulated_families | Processed Family Data
test_fam2 | Processed Family Data
transformDF | Transform Data Frame
validate_allele_freq | Validate Allele Frequency Input
validate_baseline_data | Validate Baseline Penetrance Data
validate_weibull_parameters | Validate Weibull Parameters