simulTraits12: Simul breeding game

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

Simul breeding game

Description

Simulate phenotypes of traits 1 and 2 jointly: Y = Z.J * Alpha + Z.I * G.A + E.

Usage

simulTraits12(
  dat,
  mu = c(trait1 = 100, trait2 = 15),
  sigma.alpha2 = c(trait1 = 230, trait2 = 10),
  Alpha = NULL,
  X,
  afs,
  Beta,
  h2 = NULL,
  sigma2 = c(trait1 = 330, trait2 = 0.6),
  cor.E.inter.trait = 0,
  set.neg.to.zero = TRUE,
  verbose = 1
)

Arguments

dat	data.frame specifying the structure of the initial data set of phenotypes, with columns "ind", "year", etc
mu	vector of global means, for each trait
sigma.alpha2	vector of variance for the "year" effects, for each trait (ignored if Alpha is not NULL)
Alpha	matrix of "year" effects, for each trait, the years corresponding to those indicated in dat (if NULL, will be simulated using sigma.alpha2)
X	matrix of bi-allelic SNP genotypes encoded in allele dose in 0,1,2, with individuals in rows in the same order as the levels of dat$ind
afs	vector of allele frequencies (to center X so that the genotypic values are also centered) which names are the SNPs
Beta	matrix of additive SNP effects, for each trait
h2	vector of heritabilities, with the name of each trait, for instance c(trait1=0.3, trait2=0.4) (if NULL, sigma2 will be used, but do not specify both)
sigma2	vector of error variances, with the name of each trait, for instance c(trait1=0.467, trait2=0.210) (if NULL, h2 will be used, but do not specify both)
cor.E.inter.trait	correlation of errors between both traits
set.neg.to.zero	if TRUE, the negative phenotypic values, if any, will be set to zero
verbose	verbosity level (0/1)

Value

list

Author(s)

Timothee Flutre

See Also

simulSnpEffectsTraits12, makeDfInitPhenos

Examples

## Not run: set.seed(1859)
X <- simulGenosDose(nb.genos=825, nb.snps=2000)
snp.effects12 <- simulSnpEffectsTraits12(snp.ids=colnames(X))
dat <- makeDfInitPhenos(line.ids=rownames(X))
phenos <- simulTraits12(dat, X=X, Beta=snp.effects12$Beta)
regplot(phenos$G.A[,1], phenos$G.A[,2])

## End(Not run)

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