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PCA implementation in plink
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14 months ago
prasundutta87 • 330

Hi,

Can someone point out to a document or explain how plink is calculating Principal components? I am not asking how to do it. I have already done it. I just wanted to know how is it considering the genotype values from a VCF file to calculate the principal components.

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15 months ago
United States

plink constructs the variance-standardized genetic relationship matrix ("GRM"; see Yang J, et al. "GCTA: A Tool for Genome-wide Complex Trait Analysis" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014363/ for some discussion), and extracts the top principal components from that matrix.

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Thanks a lot Christopher!!

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