How To Use Plink To Compute The Ld Between Two Sets Of Snps?
2
2
Entering edit mode
12.3 years ago
Fayue1015 ▴ 210

I have genotype data and I actually want to know the linkage relationship between two genes? So here is how I did, I map the snps which are reside to genes within +-10kb, then for two genes, each has an associated set of SNPs, how do I use plink to compute the LD between two sets of SNPs? Can I make an conclusion like this? If snp set A mapped to gene A has an average LD>0.8 with snp set B mapped to gene B, I would say gene A and gene B are linked? I find plink can only compute all pairs of LD for a given snp list. Thanks for any advice

ld snp • 5.9k views
ADD COMMENT
2
Entering edit mode
10.2 years ago

This isn't directly supported by plink. Here are two ways to reduce the filtering workload, though:

  1. Add --extract [SNP set {A+B}] --ld-snp-list [SNP set A]. It'll only be necessary to remove A-A pairs from the final report in that case.
  2. Add --extract [SNP set {A+B}] and request matrix output. The values you care about will then all be in the lower-left (or upper-right) part of the matrix.
ADD COMMENT
0
Entering edit mode
12.3 years ago
Davy ▴ 410

If you combine your two sets of SNPs into one list, and compute all pairwise LD, then simply remove all the LD values from pairs resulting from two SNPs in the same set.

You'd be best of trying something like this however with an LD mapping tool, like Haploview, and LocusZoom. How many SNPs in set A and set B are we talking about?

ADD COMMENT
0
Entering edit mode

set A and set B may contain less 100 snps, I will try Haploview and LocusZoom I do not want to use plink to do all pairwise than remove LD, too trouble some

ADD REPLY
0
Entering edit mode

Hi, are you sure Haploview or LocusZoom has such functions? It seems do not have such function to me

ADD REPLY

Login before adding your answer.

Traffic: 908 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