simulSnpEffectsTraits12: Simul breeding game

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Simul breeding game

Description

Simulate the additive SNP effects of traits 1 and 2 jointly, with some degree of pleiotropy.

Usage

simulSnpEffectsTraits12(
  snp.ids,
  sigma.beta2 = c(trait1 = 0.017, trait2 = 10^(-4)),
  prop.pleio = 0.4,
  cor.pleio = -0.7,
  verbose = 1
)

Arguments

snp.ids	vector of SNP identifiers for which effects should be simulated
sigma.beta2	vector of variances of additive SNP effects for both traits
prop.pleio	proportion of SNPs having an effect on both traits
cor.pleio	genotypic correlation at these SNPs
verbose	verbosity level (0/1)

Value

list with a matrix of SNP effects and a vector identifying which SNPs are pleiotropic

Author(s)

Timothee Flutre

Examples

## Not run: set.seed(1859)
X <- simulGenosDose(nb.genos=825, nb.snps=2000)
snp.effects <- simulSnpEffectsTraits12(snp.ids=colnames(X))
sum(snp.effects$is.pleiotropic)
regplot(snp.effects$Beta[,1], snp.effects$Beta[,2])

## End(Not run)

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.