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Question: Plotting file eigenvec
3
gravatar for danielestrife
4.2 years ago by
danielestrife • 40
Italy
danielestrife • 40 wrote:

Good morning,

i'm doing a research on GWAS and i've obtained some file.eigenvec and .eigenval after executing the command --pca on PLINK 1.9, how can i plot those files? What software can i use for this purpose?

 

Thank you in advance
file.eigenvec plink pca gwas • 3.7k views
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modified 4.2 years ago • written 4.2 years ago by danielestrife • 40

Relevant post: Gwas Stepwise Tutorial

ADD REPLY • link written 4.2 years ago by zx8754 ♦ 4.6k
7
gravatar for chrchang523
4.2 years ago by
chrchang523 ♦ 3.6k
United States
chrchang523 ♦ 3.6k wrote:

This is straightforward in R.

1. Load the .eigenvec file.  E.g. "eigenvec_table <- read.table('plink.eigenvec')"

2. Use plot() on the columns you're interested in.  Top eigenvector will be in column 3, second eigenvector will be in column 4, etc., so if you want a set of pairwise plots covering the top 4 eigenvectors, use e.g. "plot(eigenvec_table[3:6])"
ADD COMMENT • link written 4.2 years ago by chrchang523 ♦ 3.6k
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