penetrance (version 0.1.0)

lik_noSex: Likelihood Calculation without Sex Differentiation

Description

This function calculates the likelihood for an individual based on Weibull distribution parameters without considering sex differentiation.

Usage

lik_noSex(
  i,
  data,
  alpha,
  beta,
  delta,
  gamma,
  max_age,
  baselineRisk,
  BaselineNC,
  prev
)

Value

Numeric vector, containing likelihood 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 'age', 'aff' (affection status), and 'geno' (genotype).

alpha

Numeric, Weibull distribution shape parameter.

beta

Numeric, Weibull distribution scale parameter.

delta

Numeric, shift parameter for the Weibull function.

gamma

Numeric, asymptote parameter (only scales the entire distribution).

max_age

Integer, maximum age considered in the analysis.

baselineRisk

Numeric vector, baseline risk for each age.

BaselineNC

Logical, indicates if non-carrier penetrance should be based on SEER data or the calculated non-carrier penetrance.

prev

Numeric, prevalence of the risk allele in the population.