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# cageminer <img src='man/figures/logo.png' align="right" height="139" />
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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:
1. Physical proximity (or linkage disequilibrium with) trait-related
SNPs;
2. Presence in coexpression modules enriched in guide genes (i.e.,
“reference” genes that are known to be associated with the
phenotype).
3. 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](http://cran.r-project.org/). Then install `cageminer` from
[Bioconductor](http://bioconductor.org/) using the following code:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("cageminer")
```
And the development version from
[GitHub](https://github.com/almeidasilvaf/cageminer) with:
``` r
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**.
``` r
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](http://bioconductor.org/about/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](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)
through *[usethis](https://CRAN.R-project.org/package=usethis)*,
*[remotes](https://CRAN.R-project.org/package=remotes)*, and
*[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized
to use [Bioconductor’s docker
containers](https://www.bioconductor.org/help/docker/) and
*[BiocCheck](https://bioconductor.org/packages/3.15/BiocCheck)*.
- Code coverage assessment is possible thanks to
[codecov](https://codecov.io/gh) and
*[covr](https://CRAN.R-project.org/package=covr)*.
- The [documentation website](http://almeidasilvaf.github.io/cageminer)
is automatically updated thanks to
*[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
- The code is styled automatically thanks to
*[styler](https://CRAN.R-project.org/package=styler)*.
- The documentation is formatted thanks to
*[devtools](https://CRAN.R-project.org/package=devtools)* and
*[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
For more details, check the `dev` directory.
This package was developed using
*[biocthis](https://bioconductor.org/packages/3.15/biocthis)*.
