Question: Plotting file eigenvec
4
gravatar for danielestrife
4.4 years ago by
Italy
danielestrife50 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 • 3.9k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by danielestrife50

Relevant post: Gwas Stepwise Tutorial

ADD REPLYlink written 4.4 years ago by zx87544.9k
9
gravatar for chrchang523
4.4 years ago by
chrchang5233.9k
United States
chrchang5233.9k 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 COMMENTlink written 4.4 years ago by chrchang5233.9k
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