Methods for Penetrance Estimation in Family-Based Studies


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Documentation for package ‘penetrance’ version 0.1.0

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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