Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Plotting file eigenvec
4
gravatar for danielestrife
4.8 years ago by
danielestrife • 50
Italy
danielestrife • 50 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 • 4.5k views
ADD COMMENT • link •
modified 4.8 years ago • written 4.8 years ago by danielestrife • 50

Relevant post: Gwas Stepwise Tutorial

ADD REPLY • link written 4.8 years ago by zx8754 ♦ 6.6k
9
gravatar for chrchang523
4.8 years ago by
chrchang523 ♦ 4.7k
United States
chrchang523 ♦ 4.7k 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 4.8 years ago by chrchang523 ♦ 4.7k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1890 users visited in the last hour