simu_pheno: Simulate phenotypes based on genotypes.
In bcm-uga/NaturalGWAS: Simulating Phenotypes and Evaluating GWAS Methods

Description Usage Arguments Value Author(s) See Also Examples

View source: R/simulate_pheno.R

This function samples causal variants from a reference set of variants, and simulates phenotypes based on genotypes, enviromnental variables, and confounding factors.

1 2	simu_pheno(genotype, confounder, environment = NULL, ref.set, ncausal, effect.size, gxe)

`genotype`	an n by p matrix of SNP genotypes where n is the number of individuals (rows) and p is the number of SNPs (columns).
`confounder`	an object of class "confounder" created with `create_factor`.
`environment`	an environmental vector created `get_climate`.
`ref.set`	a set of weakly linked reference SNPs created with `create_refset`.
`ncausal`	number of causal variants in the simulation.
`effect.size`	effect size for causal variants in the simulation.
`gxe`	intensity of gene by environment interaction in the simulation.

A subset of 'ncausal' causal variants and a vector of phenotypes.

causal.set subset of 'ncausal' causal variants.

phenotype vector of phenotypes.

Olivier François

create_refset create_factor get_climate

library(naturalgwas)

## Load A. thaliana example
data(A.thaliana)
env <- get_climate(A.thaliana$coord)
confounder <- create_factor(A.thaliana$genotype, K = 20)
ref.set <- create_refset(A.thaliana$chrpos, window = 101)
sim.ph <- simu_pheno(A.thaliana$genotype,
                     confounder,
                     env, ref.set,
                     ncausal = 8,
                     effect.size = 20,
                     gxe = 1)