RepeatABEL (version 1.1)

simulate_PhenData: Simulation function for the RepeatABEL package.

Description

The function takes a GenABEL object as input and generates simulated phenotypic values for related individuals having repeated obserevations.

Usage

simulate_PhenData(formula.FixedEffects = y ~ 1, genabel.data, n.obs, SNP.eff = NULL, SNP.nr = NULL, beta = NULL, VC = c(1, 1, 1), GRM = NULL, sim.gamma = FALSE)

Arguments

formula.FixedEffects

A formula including the name of the simulated variable as response, and cofactors as fixed effects.

genabel.data

A GenABEL object of class gwaa.data.

n.obs

A vector including the number of observations per individual. The length of n.obs must be equal to the number if individuals in genabel.data.

SNP.eff

The size of a simulated SNP.effect.

SNP.nr

The SNP genotype that the SNP effect is simulated on. SNP.nr=i is the i:th SNP.

beta

The simulated fixed effects. Must be equal to the number of cofactors simulated (including the intercept term).

VC

A vector of length 3 including the simulated variances of the polygenic effect, permanent environmental effect and residuals, respectively.

GRM

An optional input where the Genetic Relationship Matrix can be given. Otherwise it is computed using the GenABEL package.

sim.gamma

A logical parameter specifying whether the residuals shuld be simulated from a gamma distribution or not. If specified as TRUE then residuals are drawn from a gamma distribution with variance equal to the residual variance specified in VC[3]

Value

Returns a data frame including the simulated phenotypic values, cofactors and IDs.

Examples

data(gen.data)
 #Simulate 4 observations per individual
 set.seed(1234)
 Phen.Sim <- simulate_PhenData(y ~ age, genabel.data=gen.data,
                 n.obs=rep(4, nids(gen.data)), SNP.eff=1, SNP.nr=1000, VC=c(1,1,1))
 GWAS1 <- rGLS(y ~ age, genabel.data = gen.data, phenotype.data = Phen.Sim)
 plot(GWAS1, main="Simulated Data Results")