SNP Pruning Through PCA
I have roughly 1 million SNPs from 700 individuals and I wanted to prune the SNPs down, potentially through PLINK’s –pca command. However, I’m a little perplexed with how the eignvals/vectors I receive from the –pca command are to be used in order to prune my SNPs. Or am I completely misunderstanding? Could anyone clarify?
Below is a sample of the vectors:
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