PCA implementation in plink

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.

plink pca population

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updated 8.0 years ago by chrchang523

• written 8.0 years ago by prasundutta87

1 answer

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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written 8.0 years ago by chrchang523

Thanks a lot Christopher!!

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written 8.0 years ago by prasundutta87

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