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Question: Plotting file eigenvec
6
gravatar for danielestrife
6.2 years ago by
danielestrife • 70
Italy
danielestrife • 70 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
plink pca gwas • 6.2k views
ADD COMMENT • link •
modified 9 months ago by zx8754 ♦ 9.3k • written 6.2 years ago by danielestrife • 70

Relevant post: Gwas Stepwise Tutorial

ADD REPLY • link written 6.2 years ago by zx8754 ♦ 9.3k
10
gravatar for chrchang523
6.2 years ago by
chrchang523 ♦ 7.1k
United States
chrchang523 ♦ 7.1k 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 modified 9 months ago by zx8754 ♦ 9.3k • written 6.2 years ago by chrchang523 ♦ 7.1k

Hi Chris, Why there is a "#" in the header of plink2.eigenvec? when R read "plink2.eigenvec", "#" line will be ignored

ADD REPLY • link written 9 months ago by Shicheng Guo • 8.2k
1

That depends on how you read the file with R.

For consistency with VCF, practically all plink2-output header lines start with ‘#’.

ADD REPLY • link written 9 months ago by chrchang523 ♦ 7.1k
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