Methods for Penetrance Estimation in Family-Based Studies

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Documentation for package ‘penetrance’ version 0.1.1

• 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_weibull_parameters	Validate Weibull Parameters