Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-21T13:05:20.993Z
Comments.Text: Does it have to be in R? If not, the standard things to make a PCA from genotype matrix is plink or eigenstrat.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-21T13:15:45.367Z
Comments.Text: 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.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-21T13:55:57.270Z
Comments.Text: SNPRelate claims nearly 10x faster than plink... but I don't know.
Comments.UserDisplayName: Dan Bolser
Tags: <r><snp><plink><phylogenetics><pca>
Title: Is SNPRelate the goto package for PCA of SNP data in R?
ThreadText: # 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.  
  
  ---
  
  ## 0 answers
  
  