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