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ADPenetrance wiki

Updated 14/11/2022

The repository is maintained by Thomas Spargo (thomas.spargo@kcl.ac.uk) - please reach out with any questions.

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Welcome to the ADPenetrance wiki!

This wiki contains usage documentation for each of the R functions associated with this repository.

The adpenetrance function is used for the main steps of penetrance calculation.

getResidualRisk is a helper function to facilitate quick calculation of the risk of disease among people in sampled families not inheriting the tested variant. The output of this function is to be passed to the useG argument of adpenetrance.

checkOnsetVariability provides a function for base R plotting of age of onset distributions across two groups. This can be used to give an indication about whether penetrance estimates might be affected substantially by age of sampling when there is a large difference in onset variability between groups of people with and without the variant of interest.

simADPenetrance provides a function for performing simulation studies to test the degree to which age of sampling is expected to influence lifetime penetrance estimation across various circumstances. Users can supply the numeric output by checkOnsetVariability to the onsetRateDiff argument of simADPenetrance, indicating a certain degree of departure from equal onset variability when sampling across cohorts of people with and without a tested variant. Various other parameters are provided which can be used to customise this simulation.

Various subfunctions are utilised within simADPenetrance. These are affAtAge, bindRows, genFamily, varChars, which are used internally to pseudorandomly generate simulated sample populations.

Documentation for each function within this repository can be accessed via the sidebar on the right.