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Principal component analysis (PCA) and cluster analysis

MP Maddumage Dona Ginushika Priyadarshani Premarathne
NF Nami Fukutome
KY Kazuaki Yamasaki
FH Fumiyo Hayakawa
AN Atsushi J. Nagano
HM Hisataka Mizuno
NI Nobuo Ibaragi
YN Yukio Nagano
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Principal component analysis was performed based on the vcf file generated by the populations program. The SNPRelate program43 in the R software environment (version 3.6.2)44 converted the vcf file to a gds (genomic data structure) file, drew the PCA diagrams, and calculated the contribution ratios for each principal component. This step used only bi-allelic loci. The SNPRelate program plotted the dendrogram by considering the identity by state (IBS) pairwise distances. Images of the results were generated using the basic functions of the R software environment.

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