appendGen

Simulate genotypes for an appended pedigree to an existing pedigree with genotypes.

Simulate pedigree, genetic merits and phenotypes with random/non-random matings followed by random/non-random selection with different intensities and patterns in males and females. Genotypes can be simulated for a given pedigree, or an appended pedigree to an existing pedigree with genotypes.
Mrode, R. A. (2005) <ISBN:9780851989969, 0851989969>;
Nilforooshan, M.A. (2022) <doi:10.37496/rbz5120210131>.

Mohammad Ali Nilforooshan

pedSimulate

Pedigree, Genetic Merit, Phenotype, and Genotype Simulation

appendGen function

<dl><dt>ped</dt>
<dd>: Pedigree <code>data.frame</code> with columns for animal, sire, and dam identification.</dd>
<dt>M</dt>
<dd>: Genotype <code>data.frame</code> with rows corresponding to the initial rows of the pedigree and columns corresponding to markers.</dd>
<dt>AF</dt>
<dd>: Vector of allele frequencies at different loci for the genotypes to be simulated. If no value is provided, it will be estimated from <code>M</code>.</dd>
<dt>mut.rate</dt>
<dd>: Vector of mutation rates at different loci for the genotypes to be simulated, default = 0 for no mutation.</dd>
<dt>seed</dt>
<dd>: A numeric variable input to the random number generator for reproducible simulations,
default = `NA` for non-reproducible simulations.</dd></dl>

Arguments

Simulate genotypes for an appended pedigree — appendGen

<dl>

<dt>ped</dt>
<dd>: Pedigree <code>data.frame</code> with columns for animal, sire, and dam identification.</dd>


<dt>M</dt>
<dd>: Genotype <code>data.frame</code> with rows corresponding to the initial rows of the pedigree and columns corresponding to markers.</dd>


<dt>AF</dt>
<dd>: Vector of allele frequencies at different loci for the genotypes to be simulated. If no value is provided, it will be estimated from <code>M</code>.</dd>


<dt>mut.rate</dt>
<dd>: Vector of mutation rates at different loci for the genotypes to be simulated, default = 0 for no mutation.</dd>


<dt>seed</dt>
<dd>: A numeric variable input to the random number generator for reproducible simulations,
default = `NA` for non-reproducible simulations.</dd>

</dl>

appendGen: Simulate genotypes for an appended pedigree

Description

Usage

Value

Arguments

Details

Examples