S3_Genetic_diversity+structure.html

This file is part of "High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)".

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Barnaud, Adeline; Veltman, Margaretha; Kaczmarek, Thomas; Argout, Xavier; Vigouroux, Yves; Berthouly-Salazar, Cecile; Billot, Claire, 2024, "High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)", https://doi.org/10.23708/ETC16I, DataSuds, V1; S3_Genetic_diversity+structure.html [fileName]

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File Tags	CodeDocumentation
MD5	828d31d700d62f10b8f9fbf120f7883a
Deposit Date	2024-02-22
Metadata Release Date	2024-05-16
Publication Date	2024-05-16
Size	4.3 MB
Type	HTML
File Path	Session3_GeneticDiversityStructure/
Description	In this R tutorial, we we will take a processed VCF. First, we will explore diversity through: polymorphic SNPs (required packages: adegenet), allele frequencies (required packages: adegenet), private and shared alleles (required packages: poppr), allelic richness (required packages: hierfstat), heterozygosity (required packages: hierfstat), and genetic differentiation (required packages: hierfstat). We will also illustrate how to summarise genetic diversity in a distance matrix (required packages: poppr), a phylogenetic tree (required packages: poppr, ape), a principal component analysis (required packages: adegenet), and a discriminant analysis of principal components (required packages: adegenet). Finally, we will dive deeper into the detection of population structure and loci under selection with: ancestry coefficient estimation (required packages: LEA and tess3r) and Fst outliers (required packages: OutFLANK). The Data dictionary is included in the file.

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This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

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Data and documentations are licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License.

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