Set phenotypes
Sets phenotypes for all traits by adding random error from a multivariate normal distribution.
setPheno( pop, h2 = NULL, H2 = NULL, varE = NULL, reps = 1, fixEff = 1L, p = NULL, onlyPheno = FALSE, simParam = NULL )
pop |
an object of |
h2 |
a vector of desired narrow-sense heritabilities for each trait. See details. |
H2 |
a vector of desired broad-sense heritabilities for each trait. See details. |
varE |
error (co)variances for traits. See details. |
reps |
number of replications for phenotype. See details. |
fixEff |
fixed effect to assign to the population. Used by genomic selection models only. |
p |
the p-value for the environmental covariate used by GxE traits. If NULL, a value is sampled at random. |
onlyPheno |
should only the phenotype be returned, see return |
simParam |
an object of |
There are three arguments for setting the error variance of a phenotype: h2, H2, and varE. The user should only use one of these arguments. If the user supplies values for more than one, only one will be used according to order in which they are listed above.
The h2 argument allows the user to specify the error variance according to narrow-sense heritability. This calculation uses the additive genetic variance and total genetic variance in the founder population. Thus, the heritability relates to the founder population and not the current population.
The H2 argument allows the user to specify the error variance according to broad-sense heritability. This calculation uses the total genetic variance in the founder population. Thus, the heritability relates to the founder population and not the current population.
The varE argument allows the user to specify the error variance directly. The user may supply a vector describing the error variance for each trait or supply a matrix that specify the covariance of the errors.
The reps parameter is for convient representation of replicated data. It is intended to represent replicated yield trials in plant breeding programs. In this case, varE is set to the plot error and reps is set to the number of plots per entry. The resulting phenotype represents the entry-means.
Returns an object of Pop-class or
HybridPop-class if onlyPheno=FALSE, if
onlyPheno=TRUE a matrix is returned
#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10) #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) #Create population pop = newPop(founderPop, simParam=SP) #Add phenotype with error variance of 1 pop = setPheno(pop, varE=1)
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