AlphaSimR (version 0.10.0)

SimParam_addTraitAEG: Add additive and epistasis GxE traits

Description

Randomly assigns eligble QTLs for one or more additive and epistasis GxE traits. If simulating more than one trait, all traits will be pleiotrophic with correlated effects.

Arguments

nQtlPerChr

number of QTLs per chromosome. Can be a single value or nChr values.

mean

a vector of desired mean genetic values for one or more traits

var

a vector of desired genetic variances for one or more traits

relAA

the relative variance of additive-by-additive effects compared to the additive effects

varGxE

a vector of total genotype-by-environment variances for the traits

varEnv

a vector of environmental variances for one or more traits

corA

a matrix of correlations between additive effects

corAA

a matrix of correlations between additive-by-additive effects

corGxE

a matrix of correlations between GxE effects

useVarA

tune according to additive genetic variance if true. If FALSE, tuning is performed according to total genetic variance.

gamma

should a gamma distribution be used instead of normal

shape

the shape parameter for the gamma distribution

force

should the check for a running simulation be ignored. Only set to TRUE if you know what you are doing.

Usage

SP$addTraitAG(nQtlPerChr, mean = 0, var = 1, relAA = 0, varGxE = 1e-6, varEnv = 0, corA = NULL, corAA = NULL, corGxE = NULL, useVarA = TRUE, gamma = FALSE, shape = 1)

Examples

# NOT RUN {
#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$addTraitAEG(10, varGxE=2)

# }