MapPop-class

[,MapPop-method

c,MapPop-method

isMapPop

Extends <code>RawPop-class</code> to add a genetic map.
This is the first object created in a simulation. It is used
for creating initial populations and setting traits in the
<code>SimParam</code>.

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

Ros Craddock

MapPop-class function

<dl><dt>x</dt>
<dd>a 'MapPop' object</dd>
<dt>i</dt>
<dd>index of individuals</dd>
<dt>...</dt>
<dd>additional 'MapPop' objects</dd></dl>

Arguments

<ul>
<li><code>[</code>: Extract MapPop by index</li>
<li><code>c(MapPop)</code>: Combine multiple MapPops</li>
</ul>

Methods (by generic)

<ul>
<li><code>isMapPop()</code>: Test if object is of a MapPop class</li>
</ul>

Functions

<dl>
<dt><code>genMap</code></dt>
<dd>list of chromosome genetic maps</dd></dl>
<dt><code>centromere</code></dt>
<dd>vector of centromere positions</dd>
<dt><code>inbred</code></dt>
<dd>indicates whether the individuals are fully inbred</dd>

Slots

Raw population with genetic map — MapPop-class

<dl>

<dt>x</dt>
<dd>a 'MapPop' object</dd>


<dt>i</dt>
<dd>index of individuals</dd>


<dt>...</dt>
<dd>additional 'MapPop' objects</dd>

</dl>

<dl>
<dt><code>genMap</code></dt>
<dd>list of chromosome genetic maps</dd>


<dt><code>centromere</code></dt>
<dd>vector of centromere positions</dd>


<dt><code>inbred</code></dt>
<dd>indicates whether the individuals are fully inbred</dd>


</dl>

MapPop-class: Raw population with genetic map

Description

Usage

Arguments

Methods (by generic)

Functions

Slots