<p>I'm trying to evaluate a method that I'm not familiar with. They used SNPRelate. I'm wondering if this is the best / only choice... what other tools would you recommend?</p>
<p>Many thanks,</p>

CC BY-SA 4.0
2021-05-21T13:05:20.993Z
Does it have to be in R? If not, the standard things to make a PCA from genotype matrix is plink or eigenstrat.
user438383
CC BY-SA 4.0
2021-05-21T13:15:45.367Z
That said, unless you are doing fancy stuff like PCA projection - PCA is just PCA and whilst methods might differ in terms of computational compexity, the resulting eigenvectors will be mostly very similar.
user438383
CC BY-SA 4.0
2021-05-21T13:55:57.270Z
SNPRelate claims nearly 10x faster than plink... but I don't know.
Dan Bolser
<r><snp><plink><phylogenetics><pca>
Is SNPRelate the goto package for PCA of SNP data in R?
# Is SNPRelate the goto package for PCA of SNP data in R?

(Asked by: username_0 on 2021-05-21)

I'm trying to evaluate a method that I'm not familiar with. They used SNPRelate. I'm wondering if this is the best / only choice... what other tools would you recommend?

Many thanks,

**Tags:** r, snp, plink, phylogenetics, pca
> **Comments:**
> **username_1**: Does it have to be in R? If not, the standard things to make a PCA from genotype matrix is plink or eigenstrat.  
> **username_1**: That said, unless you are doing fancy stuff like PCA projection - PCA is just PCA and whilst methods might differ in terms of computational compexity, the resulting eigenvectors will be mostly very similar.  
> **username_0**: SNPRelate claims nearly 10x faster than plink... but I don't know.  

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