SimPheno2: Simulation of phenotypic values
In vincentgarin/mppSim: Functions for simulation in MPP

SimPheno2

R Documentation

Simulation of phenotypic values

Description

Function simulating phenotypic values based on polygenic, QTL and (environmental) error component. The simulation admit 8 types of QTLs: Q1 has a different allele in each cross; Q2 segregates in half of the crosses with a different allelic value; Q3 has a different allele for each parent; Q4 has a unique allele hold by a single parent; Q5 has a different allele for each ancestral group; Q6 has a unique allele hold by the most frequent ancestral group; Q7 and Q8 are bi-allelic QTLs attached to a SNP marker.

Usage

SimPheno2(QTL, k = 1, her, mppData, cross_frac = c(0.5, 0.33))

Arguments

`QTL`	list of QTL position obtained with function `QposSelect`
`k`	Factor representing the ration between QTL (VQ) and polygenic (Vg) variance (VQ = k * Vg). Default = 1.
`her`	heritability.
`mppData`	`mppData` object
`cross_frac`	Two values vector indicating the fraction of cross with non-zero value for the cross-specific QTLs Q1 and Q2.

Value

List with the simulated phenotypic values, each contribution (polygenic, QTL, error), and the proportions of polygenic, QTL, error, QTL covariance, covariance between QTL and polygenic, etc. And also a list of extended QTLs effect with the proportion of non-zero QTL effect contribution (~ QTL allele frequency estimation).