mhLogLikelihood_clipp: Calculate Log Likelihood using clipp Package

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

Calculate Log Likelihood using clipp Package

Description

Calculate Log Likelihood using clipp Package

Usage

mhLogLikelihood_clipp(
  paras,
  families,
  twins,
  max_age,
  baseline_data,
  prev,
  geno_freq,
  trans,
  BaselineNC,
  ncores
)

Arguments

paras	Numeric vector of parameters
families	Data frame of pedigree information
twins	Information on monozygous twins
max_age	Integer, maximum age
baseline_data	Numeric matrix of baseline risk data
prev	Numeric, prevalence
geno_freq	Numeric vector of frequencies
trans	Numeric matrix of transmission probabilities
BaselineNC	Logical for baseline choice
ncores	Integer for parallel computation

Value

Numeric value representing the calculated log likelihood.

Examples

# Create example parameters and data
paras <- c(0.8, 0.7, 20, 25, 50, 45, 30, 35)  # Example parameters

# Create sample data in PanelPRO format
families <- data.frame(
  ID = 1:10,
  PedigreeID = rep(1, 10),
  Sex = c(0, 1, 0, 1, 0, 1, 0, 1, 0, 1),  # 0=female, 1=male
  MotherID = c(NA, NA, 1, 1, 3, 3, 5, 5, 7, 7),
  FatherID = c(NA, NA, 2, 2, 4, 4, 6, 6, 8, 8),
  isProband = c(1, rep(0, 9)),
  CurAge = c(45, 35, 55, 40, 50, 45, 60, 38, 52, 42),
  isAff = c(1, 0, 1, 0, 1, 0, 1, 0, 1, 0),
  Age = c(40, NA, 50, NA, 45, NA, 55, NA, 48, NA),
  Geno = c(1, NA, 1, 0, 1, 0, NA, NA, 1, NA)
)

# Transform data into required format
families <- transformDF(families)

trans <- matrix(
  c(
    1, 0, # both parents are wild type
    0.5, 0.5, # mother is wildtype and father is a heterozygous carrier
    0.5, 0.5, # father is wildtype and mother is a heterozygous carrier
    1 / 3, 2 / 3 # both parents are heterozygous carriers
  ),
 nrow = 4, ncol = 2, byrow = TRUE
)

# Calculate log likelihood
loglik <- mhLogLikelihood_clipp(
  paras = paras,
  families = families,
  twins = NULL,
  max_age = 94,
  baseline_data = baseline_data_default,
  prev = 0.001,
  geno_freq = c(0.999, 0.001),
  trans = trans,
  BaselineNC = TRUE,
  ncores = 1
)

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