Package: penetrance 0.1.3

Sol Rosito

penetrance: Methods for Penetrance Estimation in Family-Based Studies

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) <d 10.1093/bioadv/vbaf154>.

Authors:Sol Rosito [cre], Nicolas Kubista [aut], BayesMendel Lab [aut], Giovanni Parmigiani [aut], Danielle Braun [aut], Alice Zhang [aut]

penetrance_0.1.3.tar.gz
penetrance_0.1.3.zip(r-4.7)penetrance_0.1.3.zip(r-4.6)penetrance_0.1.3.zip(r-4.5)
penetrance_0.1.3.tgz(r-4.6-any)penetrance_0.1.3.tgz(r-4.5-any)
penetrance_0.1.3.tar.gz(r-4.7-any)penetrance_0.1.3.tar.gz(r-4.6-any)
penetrance_0.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
penetrance/json (API)

# Install 'penetrance' in R:
install.packages('penetrance', repos = c('https://bayesmendel.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bayesmendel/penetrance/issues

Datasets:

On CRAN:

Conda:

5.08 score 1 stars 10 scripts 475 downloads 29 exports 11 dependencies

Last updated from:97c4e40ed7. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK146
source / vignettesOK191
linux-release-x86_64OK137
macos-release-arm64OK137
macos-oldrel-arm64OK176
windows-develOK95
windows-releaseOK96
windows-oldrelOK90
wasm-releaseOK108

Exports:absValuebaseline_data_defaultcalculate_weibull_parameterscalculateBaselinecalculateEmpiricalDensitycalculateNCPencombine_chains_noSexdistribution_data_defaultgenerate_density_plotsgenerate_summarygenerate_summary_noSeximputeAgesimputeAgesInitmakePriorsmhChainmhLogLikelihood_clipppenetranceplot_acfplot_loglikelihoodplot_pdfplot_penetranceplot_traceprintRejectionRatesprior_params_defaultrisk_proportion_defaulttransformDFvalidate_allele_freqvalidate_baseline_datavalidate_weibull_parameters

Dependencies:clippevaluatehighrkinship2knitrlatticeMASSMatrixquadprogxfunyaml

Simulation Study with penetrance
Goal | Simulated Data | Simple simulation | Comparison of estimated curves vs. data-generating curves
Rendered fromsimulation_study.Rmdusingknitr::rmarkdown

Last update: 2026-05-15
Started: 2024-08-07

Simulation study from empirical data with penetrance
Goal | Simulated Data | Simple simulation | References
Rendered fromsimulation_study_real.Rmdusingknitr::rmarkdown

Last update: 2026-05-15
Started: 2024-08-12

Using penetrance
Data | Age Imputation | Estimation Approach | Prior Specification | Estimation using penetrance | Example | References
Rendered fromusing_penetrance.Rmdusingknitr::rmarkdown

Last update: 2026-04-17
Started: 2024-08-07

Readme and manuals

Help Manual

Help pageTopics
Function to return absolute valuesabsValue
Apply Burn-Inapply_burn_in
Apply Thinningapply_thinning
Default Baseline Databaseline_data_default
Calculate Weibull Parameterscalculate_weibull_parameters
Calculate Baseline RiskcalculateBaseline
Calculate Empirical Age DensitycalculateEmpiricalDensity
Calculate Age-Specific Non-Carrier PenetrancecalculateNCPen
Combine Chains Function to combine the posterior samples from the multiple chains.combine_chains
Combine Chains for Non-Sex-Specific Estimationcombine_chains_noSex
Default Distribution Datadistribution_data_default
Draw Ages Using the Inverse CDF Method from the baseline datadrawBaseline
Draw Ages Using the Inverse CDF Method from Empirical DensitydrawEmpirical
Generate Posterior Density Plotsgenerate_density_plots
Generate Summarygenerate_summary
Generate Summary for Non-Sex-Specific Estimationgenerate_summary_noSex
Impute Missing Ages in Family-Based DataimputeAges
Initialize Age ImputationimputeAgesInit
Impute Ages for Unaffected IndividualsimputeUnaffectedAges
Likelihood Calculation without Sex Differentiationlik_noSex
Penetrance Functionlik.fn
Make PriorsmakePriors
Execution of a Single Chain in Metropolis-Hastings for Cancer Risk EstimationmhChain
Calculate Log Likelihood using clipp PackagemhLogLikelihood_clipp
Calculate Log Likelihood without Sex DifferentiationmhLogLikelihood_clipp_noSex
Simulated Output Dataout_sim
penetrance: A Package for Penetrance Estimationpenetrance-package penetrance
Plot Autocorrelation for Multiple MCMC Chains (Posterior Samples)plot_acf
Plot Log-Likelihood for Multiple MCMC Chainsplot_loglikelihood
Plot Weibull Probability Density Function with Credible Intervalsplot_pdf
Plot Weibull Distribution with Credible Intervalsplot_penetrance
Plot MCMC Trace Plotsplot_trace
Print MCMC Rejection RatesprintRejectionRates
Default Prior Parametersprior_params_default
Default Risk Proportionsrisk_proportion_default
Processed Family Datasimulated_families
Processed Family Datatest_fam2
Transform Data FrametransformDF
Validate Allele Frequency Inputvalidate_allele_freq
Validate Baseline Penetrance Datavalidate_baseline_data
Validate Weibull Parametersvalidate_weibull_parameters