getGenMap

Retrieves the genetic map for all loci.

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

getGenMap function

<dl><dt>object</dt>
<dd>where to retrieve the genetic map. 
Can be an object of <code>SimParam</code> or 
<code>MapPop-class</code>. If NULL, the function will 
look for a SimParam object called "SP" in your 
global environment.</dd>
<dt>sex</dt>
<dd>determines which sex specific map 
is returned. Options are "A" for average map, "F" 
for female map, and "M" for male map. All options are 
equivalent if not using sex specific maps or using 
pulling from a MapPop.</dd></dl>

Arguments

Get genetic map — getGenMap

<dl>

<dt>object</dt>
<dd>where to retrieve the genetic map. 
Can be an object of <code>SimParam</code> or 
<code>MapPop-class</code>. If NULL, the function will 
look for a SimParam object called "SP" in your 
global environment.</dd>


<dt>sex</dt>
<dd>determines which sex specific map 
is returned. Options are "A" for average map, "F" 
for female map, and "M" for male map. All options are 
equivalent if not using sex specific maps or using 
pulling from a MapPop.</dd>

</dl>

getGenMap: Get genetic map

Description

Usage

Value

Arguments

Examples