The goal of cageminer is to integrate SNP data from GWAS results with gene coexpression networks to identify high-confidence candidate genes involved in a particular phenotype. To identify high-confidence candidate genes, cageminer considers 3 criteria:
- Physical proximity (or linkage disequilibrium with) trait-related SNPs;
- Presence in coexpression modules enriched in guide genes (i.e., “reference” genes that are known to be associated with the phenotype).
- Significant altered expression levels in a condition of interest (e.g., stress, disease, etc).
By default, cageminer defines genes as high-confidence candidates if they satisfy all of the 3 criteria above, but users can choose to use only one/some of them.
Installation instructions
Get the latest stable R release from CRAN. Then install cageminer from Bioconductor using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("cageminer")And the development version from GitHub with:
BiocManager::install("almeidasilvaf/cageminer")Citation
Below is the citation output from using citation('cageminer') in R. Please run this yourself to check for any updates on how to cite cageminer.
print(citation('cageminer'), bibtex = TRUE)
#>
#> To cite cageminer in publications use:
#>
#> Almeida-Silva, F., & Venancio, T. M. (2022). cageminer: an
#> R/Bioconductor package to prioritize candidate genes by integrating
#> genome-wide association studies and gene coexpression networks. in
#> silico Plants, 4(2), diac018.
#> https://doi.org/10.1093/insilicoplants/diac018
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {cageminer: an R/Bioconductor package to prioritize candidate genes by integrating genome-wide association studies and gene coexpression networks},
#> author = {Fabricio Almeida-Silva and Thiago M. Venancio},
#> journal = {in silico Plants},
#> year = {2022},
#> volume = {4},
#> number = {2},
#> pages = {diac018},
#> url = {https://doi.org/10.1093/insilicoplants/diac018},
#> doi = {10.1093/insilicoplants/diac018},
#> }Code of Conduct
Please note that the cageminer project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Development tools
- Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
- Code coverage assessment is possible thanks to codecov and covr.
- The documentation website is automatically updated thanks to pkgdown.
- The code is styled automatically thanks to styler.
- The documentation is formatted thanks to devtools and roxygen2.
For more details, check the dev directory.
This package was developed using biocthis.