XSim.jl

Documentation for XSim.jl

Features

• Efficient CPOS algorithm
• Founders characterized by real genome sequence data
• Complicated pedigree structures among descendants
• Strong extensibilty
• Modularism design
• Straightforward interface

Installation

julia> using Pkg
julia> Pkg.add("XSim")

or the beta version

julia> Pkg.add(PackageSpec(name="XSim", rev="master"))

Outline

Home

• XSim.jl
• Features
• Installation
• Outline
• Cite XSimV2

Demo

• Demo: Step by Step
• Step 0. Load XSim
• Step 1. Setup Genome and Phenome
• Step 2. Initialize Founders
• Step 3. Mating
• Step 4. Selection
• Step 5. Expand to Multiple Generations
• Complete Codes

Core Functions

• Build Genome
• Quick Start
• Build by a File or a DataFrame
• Build by Pre-Loaded Genome
• Build by Explicit Definition

• Build Phenome
• Quick Start
• Build by a File or a DataFrame
• Build by QTL Effects

• Cohort and Founders
• Initialize by Population Size
• Initialize by Genotypes/Haplotypes Files
• Properties

• Mating
• Arguments
• Outputs
• Examples

• Selection
• Arguments
• Outputs
• Examples

• Genetic Evaluation (JWAS)
• Arguments
• Outputs
• Example of the phenotypes Dataframe
• Examples
• References

• Breed: Wrap-up Function
• Arguments
• Outputs
• Examples

Case Studies

• Rotational Cross-Breeding
• References

• Nested Association Mapping
• References

Library

• Library
• Index
• Contents

Cite XSimV2

@article{cheng_xsim_2015,
	title = {XSim: Simulation of Descendants from Ancestors with Sequence Data},
	volume = {5},
	issn = {2160-1836},
	shorttitle = {XSim},
	url = {http://g3journal.org/lookup/doi/10.1534/g3.115.016683},
	doi = {10.1534/g3.115.016683},
	language = {en},
	number = {7},
	journal = {G3\&\#58; Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Cheng, Hao and Garrick, Dorian and Fernando, Rohan},
	month = jul,
	year = {2015},
	Pages = {1415--1417},
}