Package: GGoutlieR 1.0.2
GGoutlieR: Identify Individuals with Unusual Geo-Genetic Patterns
Identify and visualize individuals with unusual association patterns of genetics and geography using the approach of Chang and Schmid (2023) <doi:10.1101/2023.04.06.535838>. It detects potential outliers that violate the isolation-by-distance assumption using the K-nearest neighbor approach. You can obtain a table of outliers with statistics and visualize unusual geo-genetic patterns on a geographical map. This is useful for landscape genomics studies to discover individuals with unusual geography and genetics associations from a large biological sample.
Authors:
GGoutlieR_1.0.2.tar.gz
GGoutlieR_1.0.2.zip(r-4.5)GGoutlieR_1.0.2.zip(r-4.4)GGoutlieR_1.0.2.zip(r-4.3)
GGoutlieR_1.0.2.tgz(r-4.4-any)GGoutlieR_1.0.2.tgz(r-4.3-any)
GGoutlieR_1.0.2.tar.gz(r-4.5-noble)GGoutlieR_1.0.2.tar.gz(r-4.4-noble)
GGoutlieR_1.0.2.tgz(r-4.4-emscripten)GGoutlieR_1.0.2.tgz(r-4.3-emscripten)
GGoutlieR.pdf |GGoutlieR.html✨
GGoutlieR/json (API)
| # Install 'GGoutlieR' in R: |
| install.packages('GGoutlieR', repos = c('https://cheweichang1992.r-universe.dev', 'https://cloud.r-project.org')) |
- ggoutlier_example - Example of 'ggoutlier' output
- ipk_anc_coef - Ancestry coefficients of IPK barley landraces
- ipk_geo_coord - Geographical origins of IPK barley landraces
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 11 months agofrom:83ef6c0a12. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 28 2024 |
| R-4.5-win | OK | Aug 28 2024 |
| R-4.5-linux | OK | Aug 28 2024 |
| R-4.4-win | OK | Aug 28 2024 |
| R-4.4-mac | OK | Aug 28 2024 |
| R-4.3-win | OK | Aug 28 2024 |
| R-4.3-mac | OK | Aug 28 2024 |
Exports:ggoutlierggoutlier_compositeKNNggoutlier_geneticKNNggoutlier_geoKNNplot_ggoutliersummary_ggoutlier
Dependencies:askpassassertthatclassclassIntclicodetoolscolorspacecowplotcpp11curlDBIdoParalleldplyre1071fansifarverFastKNNforeachgenericsggforceggplot2gluegtablehttrisobanditeratorsjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpdistpillarpkgconfigpolyclipproxypurrrR6RColorBrewerRcppRcppEigenrlangrnaturalearths2scalessfstringistringrsyssystemfontsterratibbletidyrtidyselecttweenrunitsutf8vctrsviridisLitewithrwk
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calculate genetic similarity from ancestry coefficients. | anc_coeff_to_GeneticSimilarityMatrix |
| obtain an adjacency matrix to make a network graph | get_GGNet_adjacency_matrix |
| Identify outliers with unusual geo-genetic patterns | ggoutlier |
| GGoutlieR with the composite approach | ggoutlier_compositeKNN |
| Example of `ggoutlier` output | ggoutlier_example |
| GGoutlieR with the genetic KNN approach | ggoutlier_geneticKNN |
| GGoutlieR with the geographical KNN approach | ggoutlier_geoKNN |
| Ancestry coefficients of IPK barley landraces | ipk_anc_coef |
| Geographical origins of IPK barley landraces | ipk_geo_coord |
| Visualize GGoutlieR results on a geographical map | plot_ggoutlier |
| Summarize GGoutlieR results | summary_ggoutlier |
