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Question: PCA implementation in plink
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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.

ADD COMMENTlink 16 months ago prasundutta87 • 330 • updated 16 months ago chrchang523 5.2k
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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.

ADD COMMENTlink 16 months ago chrchang523 5.2k
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Thanks a lot Christopher!!

ADD REPLYlink 16 months ago
prasundutta87
• 330

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