https://github.com/kullrich/vgwas
Variance Heterogeneity Genome-wide Association Study - Reimplementation
https://github.com/kullrich/vgwas
gwas vgwas
Last synced: 6 months ago
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Variance Heterogeneity Genome-wide Association Study - Reimplementation
- Host: GitHub
- URL: https://github.com/kullrich/vgwas
- Owner: kullrich
- Created: 2019-08-22T06:34:49.000Z (almost 7 years ago)
- Default Branch: devel
- Last Pushed: 2025-05-17T22:44:32.000Z (about 1 year ago)
- Last Synced: 2025-05-17T23:24:37.072Z (about 1 year ago)
- Topics: gwas, vgwas
- Language: HTML
- Homepage: https://kullrich.github.io/vGWAS/
- Size: 3.27 MB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# vGWAS
[](CODE_OF_CONDUCT.md)
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](https://github.com/xiashen).
see the original publication
[Inheritance Beyond Plain Heritability: Variance-Controlling Genes in Arabidopsis thaliana](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002839)
some function has been added to directly perform GWAS on genotype data obtained
via [plink](https://www.cog-genomics.org/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](https://github.com/kullrich) using the [devtools](https://cran.r-project.org/web/packages/devtools/index.html) 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](https://github.com/kullrich/vGWAS/blob/master/vignettes/vGWAS.Rmd)
- [02. vGWAS plink tutorial](https://github.com/kullrich/vGWAS/blob/master/vignettes/vGWASsparse.Rmd)
## Code of Conduct - Participation guidelines
This repository adhere to [Contributor Covenant](http://contributor-covenant.org) code of conduct for in any interactions you have within this project. (see [Code of Conduct](https://github.com/kullrich/CRBHits/-/blob/devel/CODE_OF_CONDUCT.md))
See also the policy against sexualized discrimination, harassment and violence for the Max Planck Society [Code-of-Conduct](https://www.mpg.de/11961177/code-of-conduct-en.pdf).
By contributing to this project, you agree to abide by its terms.