writePlink

Writes a Pop-class to PLINK PED and MAP files. The arguments 
for this function were chosen for consistency with 
<code>RRBLUP2</code>. The base pair coordinate will the locus
position as stored in AlphaSimR and not an actual base pair 
position. This is because AlphaSimR doesn't track base pair 
positions, only relative positions for the loci used in the 
simulation.

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

writePlink function

<dl><dt>pop</dt>
<dd>an object of <code>Pop-class</code></dd>
<dt>baseName</dt>
<dd>basename for PED and MAP files.</dd>
<dt>traits</dt>
<dd>an integer indicating the trait to write, a trait name, or a
function of the traits returning a single value.</dd>
<dt>use</dt>
<dd>what to use for PLINK's phenotype field. Either phenotypes "pheno", 
genetic values "gv", estimated breeding values "ebv", breeding values "bv", 
or random values "rand".</dd>
<dt>snpChip</dt>
<dd>an integer indicating which SNP chip genotype 
to use</dd>
<dt>useQtl</dt>
<dd>should QTL genotypes be used instead of a SNP chip. 
If TRUE, snpChip specifies which trait's QTL to use, and thus these 
QTL may not match the QTL underlying the phenotype supplied in traits.</dd>
<dt>simParam</dt>
<dd>an object of <code>SimParam</code></dd>
<dt>...</dt>
<dd>additional arguments if using a function for 
traits</dd></dl>

Arguments

Writes a Pop-class as PLINK files — writePlink

<dl>

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


<dt>baseName</dt>
<dd>basename for PED and MAP files.</dd>


<dt>traits</dt>
<dd>an integer indicating the trait to write, a trait name, or a
function of the traits returning a single value.</dd>


<dt>use</dt>
<dd>what to use for PLINK's phenotype field. Either phenotypes "pheno", 
genetic values "gv", estimated breeding values "ebv", breeding values "bv", 
or random values "rand".</dd>


<dt>snpChip</dt>
<dd>an integer indicating which SNP chip genotype 
to use</dd>


<dt>useQtl</dt>
<dd>should QTL genotypes be used instead of a SNP chip. 
If TRUE, snpChip specifies which trait's QTL to use, and thus these 
QTL may not match the QTL underlying the phenotype supplied in traits.</dd>


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


<dt>...</dt>
<dd>additional arguments if using a function for 
traits</dd>

</dl>

writePlink: Writes a Pop-class as PLINK files

Description

Usage

Arguments