Genotype PCA from genotype matrix
If I have a individual x locus genotype matrix, what is the easiest way to calculate genotype principal components? Can I just use prcomp in R?
This lovely post Produce PCA bi-plot for 1000 Genomes Phase III - Version 2 goes through the process of generating a PCA from VCF files, but I wondered if I needed to use PLINK if I already had the matrix?
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I still don't know if PLINK, GEMMA, SNPRelate, etc. are doing anything other than generating a standard covariance matrix from the genotypes, and then just using that. Similar question here: https://bioinformatics.stackexchange.com/questions/4030/pca-on-genotype-matrix-with-multiple-alleles