mhLogLikelihood_clipp_noSex {penetrance} | R Documentation |
Calculate Log Likelihood without Sex Differentiation
Description
This function calculates the log likelihood for a set of parameters and data without considering sex differentiation using the clipp package.
Usage
mhLogLikelihood_clipp_noSex(
paras,
families,
twins,
max_age,
baseline_data,
prev,
geno_freq,
trans,
BaselineNC,
ncores
)
Arguments
paras |
Numeric vector, the parameters for the Weibull distribution and scaling factors. Should contain in order: gamma, delta, given_median, given_first_quartile. |
families |
Data frame, containing pedigree information with columns for 'age', 'aff' (affection status), and 'geno' (genotype). |
twins |
Information on monozygous twins or triplets in the pedigrees. |
max_age |
Integer, maximum age considered in the analysis. |
baseline_data |
Numeric vector, baseline risk data for each age. |
prev |
Numeric, prevalence of the risk allele in the population. |
geno_freq |
Numeric vector, represents the frequency of the risk type and its complement in the population. |
trans |
Numeric matrix, transition matrix that defines the probabilities of allele transmission from parents to offspring. |
BaselineNC |
Logical, indicates if non-carrier penetrance should be based on the baseline data or the calculated non-carrier penetrance. |
ncores |
Integer, number of cores to use for parallel computation. |
Value
Numeric, the calculated log likelihood.
References
Details about the clipp package and methods can be found in the package documentation.