<p>I found the <a href="https://cran.r-project.org/web/packages/LDheatmap/vignettes/LDheatmap.pdf" rel="nofollow noreferrer">LDheatmap</a> package in R very helpful at calculating linkage disequilibrium. You can make plots such as this:</p>

<p><a href="https://i.sstatic.net/kexIy.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/kexIy.jpg" alt="enter image description here"></a></p>

CC BY-SA 4.0
2020-04-15T14:06:32.783Z
2020-04-15T14:06:32.783Z
CephBirk
<p>I am interested in 20 different SNPs that all are either As or Gs, and they all occur on the same chromosome. How can I assess the co-occurrence of these SNPs? In other words, I want to know, if SNP1 is "G", does that make SNP2 to be more likely to be a "G" as well?</p>

<p>I know this is broad and I'm not looking for a script or anything so specific, just a point in the right direction. I'm working with a non-model organism, so any organism-specific application won't be useful without being able to learn the methodology.</p>

<p>Googling thus far has only brought up GWAS and similar methods of correlating a genotype and a phenotype, but not within a genotype.</p>

CC BY-SA 4.0
2020-04-13T18:54:15.367Z
Okay, just found the term "linkage disequilibirum" which should be helpful...
CephBirk
CC BY-SA 4.0
2020-04-13T22:48:02.647Z
I agree with @CephBirk that you are just looking for linkage disequilibrium. To calculate this in a simple way, it is just the Pearson correlation coefficient squared.
Phoenix Mu
<snp><gwas><correlation>
How to analyze co-occurrence of multiple SNPs?
# How to analyze co-occurrence of multiple SNPs?

(Asked by: username_0 on 2020-04-13)

I am interested in 20 different SNPs that all are either As or Gs, and they all occur on the same chromosome. How can I assess the co-occurrence of these SNPs? In other words, I want to know, if SNP1 is "G", does that make SNP2 to be more likely to be a "G" as well?

I know this is broad and I'm not looking for a script or anything so specific, just a point in the right direction. I'm working with a non-model organism, so any organism-specific application won't be useful without being able to learn the methodology.

Googling thus far has only brought up GWAS and similar methods of correlating a genotype and a phenotype, but not within a genotype.

**Tags:** snp, gwas, correlation
> **Comments:**
> **username_0**: Okay, just found the term "linkage disequilibirum" which should be helpful...  
> **username_1**: I agree with @CephBirk that you are just looking for linkage disequilibrium. To calculate this in a simple way, it is just the Pearson correlation coefficient squared.  

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## 1 answers

### Answer by username_0 on 2020-04-15. Score: 1

I found the [LDheatmap](https://cran.r-project.org/web/packages/LDheatmap/vignettes/LDheatmap.pdf) package in R very helpful at calculating linkage disequilibrium. You can make plots such as this:

[![enter image description here](https://i.sstatic.net/kexIy.jpg)](https://i.sstatic.net/kexIy.jpg)


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