Single Trait Analysis

Sinlge-trait analysis

• Univariate Linear Additive Genetic Model
• Univariate Linear Mixed Model (Genomic data)

Univariate Linear Additive Genetic Model

using JWAS, DataFrames, CSV

phenotypes   = CSV.read("phenotype.csv",delim = ',',header=true,missingstrings=["NA"]);
geno         = get_genotypes("genotypes.txt");#df=4,G_is_marker_variance=false 

model_equations = "y1 = intercept + geno
                   y2 = intercept + geno";
model           = build_model(model_equations);


@time out=runMCMC(model,data,chain_length=50_000);

##save variables
using JLD
save("results.jld", "out", out)

Univariate Linear Mixed Model (Genomic data)

tic()
out=runMCMC(model,data,Pi2);
toc()