Package: penetrance 0.1.0

Nicolas Kubista
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) <doi:10.48550/arXiv.2411.18816>.
Authors:
penetrance_0.1.0.tar.gz
penetrance_0.1.0.tar.gz(r-4.5-noble)penetrance_0.1.0.tar.gz(r-4.4-noble)
penetrance_0.1.0.tgz(r-4.4-emscripten)penetrance_0.1.0.tgz(r-4.3-emscripten)
penetrance.pdf |penetrance.html✨
penetrance/json (API)
# Install 'penetrance' in R: |
install.packages('penetrance', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nicokubi/penetrance/issues
Pkgdown site:https://nicokubi.github.io
- out_sim - Simulated Output Data
- simulated_families - Processed Family Data
- test_fam2 - Processed Family Data
Last updated 13 days agofrom:37052cbcda. Checks:3 OK. Indexed: no.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Mar 03 2025 |
R-4.5-linux | OK | Mar 03 2025 |
R-4.4-linux | OK | Mar 03 2025 |
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_weibull_parameters
Dependencies:clippevaluatehighrkinship2knitrlatticeMASSMatrixquadprogxfunyaml
Using penetrance
Rendered fromusing_penetrance.Rmd
usingknitr::rmarkdown
on Mar 03 2025.Last update: 2025-03-03
Started: 2025-03-03
Simulation study from empirical data with penetrance
Rendered fromsimulation_study_real.Rmd
usingknitr::rmarkdown
on Mar 03 2025.Last update: 2025-03-03
Started: 2025-03-03
Simulation Study with penetrance
Rendered fromsimulation_study.Rmd
usingknitr::rmarkdown
on Mar 03 2025.Last update: 2025-03-03
Started: 2025-03-03