lik.fn: Penetrance Function

Description

Calculates the penetrance for an individual based on Weibull distribution parameters. This function estimates the probability of developing cancer given the individual's genetic and demographic information.

Usage

lik.fn(
  i,
  data,
  alpha_male,
  alpha_female,
  beta_male,
  beta_female,
  delta_male,
  delta_female,
  gamma_male,
  gamma_female,
  max_age,
  baselineRisk,
  BaselineNC,
  prev
)

Value

Numeric vector, containing penetrance values for unaffected and affected individuals.

Arguments

i: Integer, index of the individual in the data set.
data: Data frame, containing individual demographic and genetic information. Must include columns for 'sex', 'age', 'aff' (affection status), and 'geno' (genotype).
alpha_male: Numeric, Weibull distribution shape parameter for males.
alpha_female: Numeric, Weibull distribution shape parameter for females.
beta_male: Numeric, Weibull distribution scale parameter for males.
beta_female: Numeric, Weibull distribution scale parameter for females.
delta_male: Numeric, shift parameter for the Weibull function for males.
delta_female: Numeric, shift parameter for the Weibull function for females.
gamma_male: Numeric, asymptote parameter for males (only scales the entire distribution).
gamma_female: Numeric, asymptote parameter for females (only scales the entire distribution).
max_age: Integer, maximum age considered in the analysis.
baselineRisk: Numeric matrix, baseline risk for each age by sex. Rows correspond to sex (1 for male, 2 for female) and columns to age.
BaselineNC: Logical, indicates if non-carrier penetrance should be based on SEER data.
prev: Numeric, prevalence of the risk allele in the population.