SimParam_addStructuredSnpChips

number of SNPs per chromosome. 
Can be a single value or nChr values.

nSnpPerChr

a matrix. Rows are snp chips, columns are chips.
If value is true then that snp is on that chip.

structure

should the check for a running simulation be 
ignored. Only set to TRUE if you know what you are doing.

force

Randomly selects the number of snps in structure and then
assigns them to chips based on structure

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

SimParam_addStructuredSnpChips function

SP$addStructuredSnpChip(nSnpPerChr, structure, force = FALSE)

SimParam_addStructuredSnpChips: Add Structured SNP chips

Description

Arguments

Usage