Obtaining all independent SNPs
1
0
Entering edit mode
13 days ago

Hi,

I wish to perform a random permutation analysis, for which I need to randomly select SNPs. I was thinking that these SNPs should ideally come from a list of all independent SNPs. Initially I thought that I could perform clumping or pruning of e.g. HapMap data in PLINK, but upon closer inspection I'm not sure this would work, as both have some kind of selection (MAF or P-value) that might introduce a bias in my independent SNP set. Not to mention the fact that I don't actually have p-values to base this on.

This random permutation analysis I'm attempting isn't new, so I'm wondering if there are existing SNP datasets of independent SNPs I could use. Or how I could best go about creating my own.

Any help is appreciated!

SNPs permutation pruning clumping PLINK • 104 views
ADD COMMENT
2
Entering edit mode
13 days ago
Sam ★ 3.6k

Based on what you want to do, I'd go with clumping, but with randomized p-value. So some pseudo R code will be

library(data.table)
dat <- fread("bim file")
fake <- dat[,c("SNP")]
for(i in 1:perm){
    fake[,P:= runif(.N, min=0, max=1)
    fwrite(fake, sep="\t")
    # Sysmtem call to clumping step
    # Your analysis here
}

Now because your p-value are randomize, clumping will generate a random set of "independent" SNPs.

ADD COMMENT

Login before adding your answer.

Traffic: 2590 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6