calculateNCPen: Calculate Age-Specific Non-Carrier Penetrance

In penetrance: Methods for Penetrance Estimation in Family-Based Studies

Calculate Age-Specific Non-Carrier Penetrance

Description

This function calculates the age-specific non-carrier penetrance based on SEER baseline data, penetrances for carriers, and allele frequencies. It adjusts penetrance estimates for genetic testing by incorporating the genetic risk attributable to specified alleles.

Usage

calculateNCPen(SEER_baseline, alpha, beta, delta, gamma, prev, max_age)

Arguments

SEER_baseline	Numeric, the baseline penetrance derived from SEER data for the general population without considering genetic risk factors.
alpha	Numeric, shape parameter for the Weibull distribution used to model carrier risk.
beta	Numeric, scale parameter for the Weibull distribution used to model carrier risk.
delta	Numeric, location parameter for the Weibull distribution used to model carrier risk.
gamma	Numeric, scaling factor applied to the Weibull distribution to adjust carrier risk.
prev	Numeric, the prevalence of the risk allele in the population.
max_age	Integer, the maximum age up to which the calculations are performed.

Value

A list containing:

weightedCarrierRisk	Numeric vector, the weighted risk for carriers at each age based on prevalence.
yearlyProb	Numeric vector, the yearly probability of not getting the disease at each age.
cumulativeProb	Numeric vector, the cumulative probability of not getting the disease up to each age.

penetrance documentation built on April 4, 2025, 12:29 a.m.