editGenomeTopQtl

Edits the top QTL (with the largest additive effect) to a homozygous
state for the allele increasing. Only nonfixed QTL are edited The gv slot is
recalculated to reflect the any changes due to editing, but other slots remain the same.

The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].

Chris Gaynor

AlphaSimR

Breeding Program Simulations

Gregor Gorjanc

John Hickey

Daniel Money

David Wilson

Thiago Oliveira

Audrey Martin

Philip Greenspoon

editGenomeTopQtl function

<dl><dt>pop</dt>
<dd>an object of <code>Pop-class</code></dd>
<dt>ind</dt>
<dd>a vector of individuals to edit</dd>
<dt>nQtl</dt>
<dd>number of QTL to edit</dd>
<dt>trait</dt>
<dd>which trait effects should guide selection of the top QTL</dd>
<dt>increase</dt>
<dd>should the trait value be increased or decreased</dd>
<dt>simParam</dt>
<dd>an object of <code>SimParam</code></dd></dl>

Arguments

Edit genome - the top QTL — editGenomeTopQtl

<dl>

<dt>pop</dt>
<dd>an object of <code>Pop-class</code></dd>


<dt>ind</dt>
<dd>a vector of individuals to edit</dd>


<dt>nQtl</dt>
<dd>number of QTL to edit</dd>


<dt>trait</dt>
<dd>which trait effects should guide selection of the top QTL</dd>


<dt>increase</dt>
<dd>should the trait value be increased or decreased</dd>


<dt>simParam</dt>
<dd>an object of <code>SimParam</code></dd>

</dl>

editGenomeTopQtl: Edit genome - the top QTL

Description

Usage

Value

Arguments

Examples