PCA implementation in plink

Question

[prasundutta87]

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.

Answer 1

[chrchang523]

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.

[prasundutta87]

Thanks a lot Christopher!!