addSegSite

This function allows for adding a new
segregating site with user supplied genotypes to a MapPop.
The position of the site is set using a genetic map position.

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

addSegSite function

<dl><dt>mapPop</dt>
<dd>an object of <code>MapPop-class</code></dd>
<dt>siteName</dt>
<dd>name to give the segregating site</dd>
<dt>chr</dt>
<dd>which chromosome to add the site</dd>
<dt>mapPos</dt>
<dd>genetic map position of site in Morgans</dd>
<dt>haplo</dt>
<dd>haplotypes for the site</dd></dl>

Arguments

Add segregating site to MapPop — addSegSite

<dl>

<dt>mapPop</dt>
<dd>an object of <code>MapPop-class</code></dd>


<dt>siteName</dt>
<dd>name to give the segregating site</dd>


<dt>chr</dt>
<dd>which chromosome to add the site</dd>


<dt>mapPos</dt>
<dd>genetic map position of site in Morgans</dd>


<dt>haplo</dt>
<dd>haplotypes for the site</dd>

</dl>

addSegSite: Add segregating site to MapPop

Description

Usage

Value

Arguments

Examples