simulate_PhenData: Simulation function for the RepeatABEL package.
In RepeatABEL: GWAS for Multiple Observations on Related Individuals

Description Usage Arguments Value Author(s) Examples

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

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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)

`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]`

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

Lars Ronnegard

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")