RawPop-class

[,RawPop-method

c,RawPop-method

show,RawPop-method

isRawPop

The raw population class contains only genotype data.

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

RawPop-class function

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

Arguments

<ul>
<li><code>[</code>: Extract RawPop by index</li>
<li><code>c(RawPop)</code>: Combine multiple RawPops</li>
<li><code>show(RawPop)</code>: Show population summary</li>
</ul>

Methods (by generic)

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

Functions

<dl>
<dt><code>nInd</code></dt>
<dd>number of individuals</dd></dl>
<dt><code>nChr</code></dt>
<dd>number of chromosomes</dd>
<dt><code>ploidy</code></dt>
<dd>level of ploidy</dd>
<dt><code>nLoci</code></dt>
<dd>number of loci per chromosome</dd>
<dt><code>geno</code></dt>
<dd>list of nChr length containing chromosome genotypes.
Each element is a three dimensional array of raw values.
The array dimensions are nLoci by ploidy by nInd.</dd>

Slots

Raw Population — RawPop-class

<dl>

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


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


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


<dt>object</dt>
<dd>a 'RawPop' object</dd>

</dl>

<dl>
<dt><code>nInd</code></dt>
<dd>number of individuals</dd>


<dt><code>nChr</code></dt>
<dd>number of chromosomes</dd>


<dt><code>ploidy</code></dt>
<dd>level of ploidy</dd>


<dt><code>nLoci</code></dt>
<dd>number of loci per chromosome</dd>


<dt><code>geno</code></dt>
<dd>list of nChr length containing chromosome genotypes.
Each element is a three dimensional array of raw values.
The array dimensions are nLoci by ploidy by nInd.</dd>


</dl>

RawPop-class: Raw Population

Description

Usage

Arguments

Methods (by generic)

Functions

Slots