writePlink

an object of <code><a rd-options="" href="/link/Pop-class?package=AlphaSimR&version=0.10.0" data-mini-rdoc="AlphaSimR::Pop-class">Pop-class</a></code>

a character. Basename of PED and MAP files.

baseName

an integer. Which phenotype trait should be used.

trait

an integer. Which SNP array should be used.

snpChip

an object of <code><a rd-options="" href="/link/SimParam?package=AlphaSimR&version=0.10.0" data-mini-rdoc="AlphaSimR::SimParam">SimParam</a></code>

simParam

an integer. The size of chromosomes in base
pairs; assuming all chromosomes are of the same size.

chromLength

Writes a Pop-class as PLINK PED and MAP files

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

David Wilson

Daniel Money

John Hickey

writePlink function

an object of <code><a rd-options='' href='Pop-class'>Pop-class</a></code>

an object of <code><a rd-options='' href='SimParam'>SimParam</a></code>

writePlink: Writes a Pop-class as PLINK files

Description

Usage

Arguments