Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis. Implements the method described in (Luu, 2016) <doi:10.1111/1755-0998.12592> and later revised in (Privé, 2020) <doi:10.1093/molbev/msaa053>.
| Version: | 4.4.1 |
| Imports: | bigutilsr (≥ 0.3),data.table,ggplot2 (≥ 3.4),magrittr,mmapcharr (≥ 0.3),Rcpp (≥ 0.12.8),RSpectra |
| LinkingTo: | mmapcharr,Rcpp,rmio |
| Suggests: | plotly,shiny,spelling,testthat,vcfR |
| Published: | 2025-07-25 |
| DOI: | 10.32614/CRAN.package.pcadapt |
| Author: | Keurcien Luu [aut], Michael Blum [aut], Florian Privé [aut, cre], Eric Bazin [ctb], Nicolas Duforet-Frebourg [ctb] |
| Maintainer: | Florian Privé <florian.prive.21 at gmail.com> |
| BugReports: | https://github.com/bcm-uga/pcadapt/issues |
| License: | GPL-2 |GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://github.com/bcm-uga/pcadapt |
| NeedsCompilation: | yes |
| Language: | en-US |
| Citation: | pcadapt citation info |
| Materials: | README,NEWS |
| In views: | AnomalyDetection |
| CRAN checks: | pcadapt results |