gwasQxE

This repository contains phenotype data, genotype data and an R package ("gwasQxE") corresponding to a manuscript titled "Exploring Efficient Linear Mixed Models to Detect Quantitative Trait Locus-by-environment Interactions" (doi: 10.1093/g3journal/jkab119). The main objective of the study was to perform genome-wide association study to detect Quantitative Trait Locus-by-environment (QxE) Interactions.

The following files are included with this distribution.

• R package: gwasQxE
• Genotype data: SL96_geno_QxE.csv
• Phenotype data: SL96_pheno_QxE.csv
• R source code for results in the manuscript: simulation_note.R

Example

Following libraries are required to perform the analyses in note.R.

require(gaston)
require(qqman)
require(gwasQxE)

The simplest code to run gwasQxE is as follows

geno = read.csv("SL96_geno_QxE.csv")
pheno = read.csv("SL96_pheno_QxE.csv")

res = gwasQxE(geno,
        pheno,
        trait = "Fruit_weight",
        Env = "season",
        n.PC = 2)

Versions

• 1.0.0 A bug when argument Env = "trial" in the function gwasQxE has been fiexd.

• 0.1.0 The first version of this repository.