https://github.com/snitkin-lab-umich/prewas
R package to perform data pre-processing for more informative bacterial GWAS
https://github.com/snitkin-lab-umich/prewas
bacterial-genomes gwas gwas-tools microbiology r r-package
Last synced: about 1 month ago
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R package to perform data pre-processing for more informative bacterial GWAS
- Host: GitHub
- URL: https://github.com/snitkin-lab-umich/prewas
- Owner: Snitkin-Lab-Umich
- License: other
- Created: 2019-10-10T14:43:59.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2023-04-07T14:44:08.000Z (about 2 years ago)
- Last Synced: 2025-03-27T03:22:29.154Z (about 2 months ago)
- Topics: bacterial-genomes, gwas, gwas-tools, microbiology, r, r-package
- Language: R
- Homepage:
- Size: 927 KB
- Stars: 5
- Watchers: 3
- Forks: 3
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# [prewas: data pre-processing for more informative bacterial GWAS](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000368)
[](https://cran.r-project.org/package=prewas)
[](https://cran.r-project.org/package=prewas)
## Introduction
The prewas R package allows users to create a binary SNP matrix from a whole genome alignment. The SNP matrix includes the following features: (1) multiple line representation of multiallelic sites, (2) multiple line representation for SNPs present in overlapping genes, and (3) choice over the reference allele. Additionally, users can collapse SNPs into genes so the output is a binary gene matrix. Output from the prewas package should be used as the input to bacterial GWAS tools such as [hogwash](https://github.com/katiesaund/hogwash).
Note: this package depends on R (>= 3.5.0).
For the most up-to-date package, it is recommended to install using dev.tools:
```
install.packages("devtools")
devtools::install_github("Snitkin-Lab-Umich/prewas")
library(prewas)
```
## Documentation
prewas is described in the paper: ["prewas: data pre-processing for more informative bacterial GWAS"](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000368). The Rscripts and data for the paper's figures and analyses can be found [in the manuscript analysis repository](https://github.com/Snitkin-Lab-Umich/prewas_manuscript_analysis).
A tutorial explaining how to use the package can be found in the [vignette](https://github.com/Snitkin-Lab-Umich/prewas/blob/master/vignettes/getting_started_with_prewas.Rmd).
## Contributors
[Katie Saund](https://github.com/katiesaund), [Stephanie Thiede](https://github.com/sthiede), and [Zena Lapp](https://github.com/zenalapp) contributed to this code.
## Questions
Please open an [issue](https://github.com/Snitkin-Lab-Umich/prewas/issues) or contact Evan Snitkin ([email protected]) with any questions.