pullIbdHaplo

an object of <code><a rd-options="" href="/link/Pop-class?package=AlphaSimR&version=0.8.2" data-mini-rdoc="AlphaSimR::Pop-class">Pop-class</a></code> or 
<code><a rd-options="" href="/link/RawPop-class?package=AlphaSimR&version=0.8.2" data-mini-rdoc="AlphaSimR::RawPop-class">RawPop-class</a></code>. If NULL, haplotypes for the whole
ancestral pedigree are retreived. Otherwise, haplotypes just for
the <code>pop</code> individuals are retreived. In both cases the base
population is controlled by <code>pedigree</code>.

a vector of chromosomes to retrieve. If NULL, 
all chromosomes are retrieved.

an integer. Indicates which SNP array loci
are retrieved. If NULL, all sites are retrieved.

snpChip

a matrix with ancestral pedigree to set a base
population. It should be of the same form as <code>simParam$pedigree</code> 
(see <code><a rd-options="" href="/link/SimParam_setTrackPed?package=AlphaSimR&version=0.8.2" data-mini-rdoc="AlphaSimR::SimParam_setTrackPed">SimParam_setTrackPed</a></code>), i.e., two columns (mother
and father) and the same number of rows as <code>simParam$pedigree</code>.
Base population can be set by setting parents as 0. If NULL, pedigree
from <code><a rd-options="" href="/link/SimParam?package=AlphaSimR&version=0.8.2" data-mini-rdoc="AlphaSimR::SimParam">SimParam</a></code> is taken.

pedigree

an object of <code><a rd-options="" href="/link/SimParam?package=AlphaSimR&version=0.8.2" data-mini-rdoc="AlphaSimR::SimParam">SimParam</a></code>

simParam

Retrieves Identity By Descent (IBD) haplotype 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

David Wilson

Daniel Money

John Hickey

pullIbdHaplo function

an object of <code><a rd-options='' href='Pop-class'>Pop-class</a></code> or 
<code><a rd-options='' href='RawPop-class'>RawPop-class</a></code>. If NULL, haplotypes for the whole
ancestral pedigree are retreived. Otherwise, haplotypes just for
the <code>pop</code> individuals are retreived. In both cases the base
population is controlled by <code>pedigree</code>.

a matrix with ancestral pedigree to set a base
population. It should be of the same form as <code>simParam$pedigree</code> 
(see <code><a rd-options='' href='SimParam_setTrackPed'>SimParam_setTrackPed</a></code>), i.e., two columns (mother
and father) and the same number of rows as <code>simParam$pedigree</code>.
Base population can be set by setting parents as 0. If NULL, pedigree
from <code><a rd-options='' href='SimParam'>SimParam</a></code> is taken.

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

pullIbdHaplo: Pull Identity By Descent (IBD) haplotypes

Description

Usage

Arguments

Value