README.md

In kullrich/vGWAS: Variance Heterogeneity Genome-wide Association Study - Reimplementation

vGWAS

Variance Heterogeneity Genome-wide Association Study - Reimplementation

R package source code: https://github.com/kullrich/vGWAS

R package pages: https://kullrich.github.io/vGWAS/

R package issues: https://github.com/kullrich/vGWAS/issues

This repository is a reimplementation from the original vGWAS R package from Xia Shen.

see the original publication Inheritance Beyond Plain Heritability: Variance-Controlling Genes in Arabidopsis thaliana

some function has been added to directly perform GWAS on genotype data obtained via plink

the function vGWASparallel has been added to perform statistical tests in parallel and work on genotype data encoded as sparse matrix

Installation

R specific installation prerequisites

install.packages("devtools")
install.packages("knitr")
install.packages("dglm")
install.packages("doParallel")
install.packages("foreach")
install.packages("genio")
install.packages("hglm")
install.packages("Matrix")
install.packages("onewaytests")

Install vGWAS package from github using the devtools package.

library(devtools)
devtools::install_github("kullrich/vGWAS", build_vignettes = TRUE, dependencies = FALSE)

Quick start

library(vGWAS)
data(pheno)
data(geno.sparse)
data(chr)
data(map)
vgwa <- vGWASparallel(
  phenotype = pheno,
  geno.matrix = geno.sparse,
  marker.map = map,
  chr.index = chr,
  geno.snp = "row"
)
plot(vgwa)

Vignettes

These vignettes introduce vGWAS

• 01. vGWAS basic tutorial
• 02. vGWAS plink tutorial

Code of Conduct - Participation guidelines

This repository adhere to Contributor Covenant code of conduct for in any interactions you have within this project. (see Code of Conduct)

See also the policy against sexualized discrimination, harassment and violence for the Max Planck Society Code-of-Conduct.

By contributing to this project, you agree to abide by its terms.

kullrich/vGWAS documentation built on June 10, 2025, 3:56 a.m.