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

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Vignette - vGWAS plink tutorial

A Brief Tutorial of the R Package vGWAS using sparse genotype data

Setup Notes

To use the vGWAS package, of course, an R environment is required. Visit:

http://www.r-project.org

and install R for the operating system.

Start R and in the R console, type the following command to install the package dependencies first:

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

Now the package is installed in the R library.

Example

It is assumed that genotype data is encoded as follows:

0: Homozygous ref allele 1: Heterozygous 2: Homozygous alt allele

Pre-processing can be done with e.g.

Remarks

The package source and further development information are on the R-Forge project page: https://r-forge.r-project.org/projects/vgwas/

A reimplementation of vGWAS introducing the parallel function vGWASparallel as a devtool package can be found here: https://github.com/kullrich/vGWAS

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