anc_coeff_to_GeneticSimilarityMatrix

calculate genetic similarity from ancestry coefficients.

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.

Che-Wei Chang

GGoutlieR

Identify Individuals with Unusual Geo-Genetic Patterns

Karl Schmid

anc_coeff_to_GeneticSimilarityMatrix function

<dl><dt>anc_coef</dt>
<dd>a matrix of ancestry coefficients with samples by rows. Each column corresponds to an ancestral population.</dd></dl>

Arguments

calculate genetic similarity from ancestry coefficients. — anc_coeff_to_GeneticSimilarityMatrix

<dl>

<dt>anc_coef</dt>
<dd>a matrix of ancestry coefficients with samples by rows. Each column corresponds to an ancestral population.</dd>

</dl>

anc_coeff_to_GeneticSimilarityMatrix: calculate genetic similarity from ancestry coefficients.

Description

Usage

Arguments

Details