JWAS.jl

JWAS.jl is an open-source software tool written in Julia for Bayesian multiple regression methods applied to genomic prediction and genome-wide association studies.

• Homepage: QTL.rocks
• Discussion group: available here
• Installation: at the Julia REPL, using Pkg; Pkg.add("JWAS")
• Documentation: manual and workflow guidance
• Examples: available on the JWAS wiki
• Authors: Hao Cheng, Tianjing Zhao, Rohan Fernando, Dorian Garrick

Structure of JWAS

  flowchart TD;
      A["phenotypes.csv"] --> A2(CSV.read) --> D(build_model)
      B["pedigree.csv"] --> B2(get_pedigree) --> D(build_model)
      C["genotypes.csv"] --> C2(get_genotypes) --> D(build_model)
      D --> E(set_covariate);
      D --> F(set_random);
      E --> H{runMCMC}
      F --> H

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Help

1. Show this README file in REPL or notebook using ?JWAS
2. For help on a specific function above, type ? followed by its name, e.g. ?runMCMC and press enter.
3. Run Pkg.add(PackageSpec(name="JWAS", rev="master")) to get the newest unofficial JWAS. Run Pkg.free("JWAS") to go back to the official one.

Examples

The JWAS documentation contains the current manual and workflow guidance. Full example analyses are available on the wiki.

• Single Trait Analysis
• Multiple Trait Analysis
• Repeated Measures
• Single Step Analysis
• Categorical Trait Analysis
• Censored Trait Analysis
• Joint Analysis of Continuous, Categorical, and Censored Traits
• Multi-class Bayesian Analysis
• Cross Validation
• Genome Wide Association Study
• Integrating Phenotypic Causal Networks in GWAS
• single trait and multiple trait GBLUP by providing the relationship matrix directly
• Description of Mixed Effects Model
• Quality Control of Genotypes