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GGoutlieR (version 1.0.2)

Identify Individuals with Unusual Geo-Genetic Patterns

Description

Identify and visualize individuals with unusual association patterns of genetics and geography using the approach of Chang and Schmid (2023) . 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.

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Version

Install

install.packages('GGoutlieR')

Monthly Downloads

179

Version

1.0.2

License

MIT + file LICENSE

Maintainer

Che-Wei Chang

Last Published

October 15th, 2023

Functions in GGoutlieR (1.0.2)

ggoutlier_example

Example of `ggoutlier` output
ggoutlier_compositeKNN

GGoutlieR with the composite approach
anc_coeff_to_GeneticSimilarityMatrix

calculate genetic similarity from ancestry coefficients.
plot_ggoutlier

Visualize GGoutlieR results on a geographical map
get_GGNet_adjacency_matrix

obtain an adjacency matrix to make a network graph
ipk_anc_coef

Ancestry coefficients of IPK barley landraces
ggoutlier_geneticKNN

GGoutlieR with the genetic KNN approach
ipk_geo_coord

Geographical origins of IPK barley landraces
ggoutlier_geoKNN

GGoutlieR with the geographical KNN approach
ggoutlier

Identify outliers with unusual geo-genetic patterns
summary_ggoutlier

Summarize GGoutlieR results