plink 1.9 Principal Component Analysis
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7.4 years ago
peris ▴ 120

Hi all,

I have done a plink pca test on my cas/control samples and generated *.eigenval and *.eigenvec files. Now how can I identify the outliers. I am not comfortable in using EIGENSOFT. Is there any other way to do the same.

Thanks and regards.

pca plink • 6.7k views
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Hi, did you find out how to plot the eigenvec? I know you can use plot() but how can one add the sample labels?

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7.4 years ago

You should be able to load the .eigenvec file in R, perform clustering on it, and identify outliers in the process.

(The old PLINK way to do this was the --neighbour command. This was based on a basic identity-by-state matrix instead of the variance-normalized GRM, but results should be similar.)

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Hi chrchang523, thanks for your reply. I need some tip from you again. I know very little R and very very new in GWAS related studies. I can plot grap from the PCA using R; but how can I perform clustering for identifying the outliers.

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A large number of clustering routines have been written for R.  http://cran.r-project.org/web/views/Cluster.html is a reasonable starting point.

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