- N.fam
Number of families to generate.
- N.sim
Number of simulations.
- effectsize
Effect size of the major mutated gene (beta.gene) to detect under the alternative hypothesis. When interaction=TRUE, both the main and interaction effects should be specified, effectsize = c(beta.gene, beta.int).
- beta.sex
Gender effect that is fixed in the model.
- alpha
Significance level. Default value is 0.05.
- side
Number of sides for the alternative hypothesis. Possible choices are 1 for one-sided test and 2 for two-sided test. Default value is 2.
- design
Family based study design used in the simulations. Possible choices are: "pop", "pop+", "cli", "cli+" or "twostage", where "pop" is for the population-based design that families are ascertained by affected probands, "pop+" is similar to "pop" but with mutation carrier probands, "cli" is for the clinic-based design that includes affected probands with at least one parent and one sibling affected, "cli+" is similar to "cli" but with mutation carrier probands and "twostage" for two-stage design that randomly samples families from the population in the first stage and oversamples high risk families in the second stage that includes at least two affected members in the family. Default is "pop".
- variation
Source of residual familial correlation. Possible choices are: "frailty" for frailty shared within families, "secondgene" for second gene variation, or "none" for no residual familial correlation. Default is "none".
- interaction
Logical; if TRUE, the interaction between gender and mutation status is allowed, otherwise no interaction is allowed. Default is FALSE.
- depend
Variance of the frailty distribution. Dependence within families increases with depend value. Default value is NULL. Value > 0 should be specified when variation = "frailty".
- base.dist
Choice of baseline hazard distribution. Possible choices are: "Weibull", "loglogistic", "Gompertz", "lognormal" "gamma", or "logBurr". Default is "Weibull".
- frailty.dist
Choice of frailty distribution. Possible choices are: "gamma" for gamma distribution or "lognormal" for log normal distribution when variation = "frailty". Default is NULL.
- base.parms
Vector of parameter values for baseline hazard function.
base.parms = c(lambda, rho), where lambda and rho are the shape and scale parameters, respectively. If base.dist = "logBurr" is chosen, three parameters should be specified for base.parms = c(lambda, rho, eta).
- allelefreq
Vector of population allele frequencies of major and second disease gene alleles. Frequencies must be between 0 and 1. Default frequencies are 0.02 for major gene allele and 0.2 for second gene allele, allelefreq = c(0.02, 0.2).
- dominant.m
Logical; if TRUE, the genetic model of the major gene is dominant, otherwise recessive.
- dominant.s
Logical; if TRUE, the genetic model of the second gene is dominant, otherwise recessive.
- mrate
Proportion of missing genotypes, value between 0 and 1. Default value is 0.
- hr
Proportion of high risk families, which include at least two affected members, to be sampled from the two stage sampling. This value should be specified when design = "twostage". Default value is 0. Value should lie between 0 and 1.
- probandage
Vector of mean and standard deviation for the proband age. Default values are mean of 45 years and standard deviation of 2 years, probandage = c(45, 2).
- agemin
Minimum age of disease onset or minimum age. Default is 20 years of age.
- agemax
Maximum age of disease onset or maximum age. Default is 100 years of age.