Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-15T14:06:32.783Z
Answers.LastActivityDate: 2020-04-15T14:06:32.783Z
Answers.UserDisplayName: CephBirk
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-13T18:54:15.367Z
Comments.Text: Okay, just found the term "linkage disequilibirum" which should be helpful...
Comments.UserDisplayName: CephBirk
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-13T22:48:02.647Z
Comments.Text: 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.
Comments.UserDisplayName: Phoenix Mu
Tags: <snp><gwas><correlation>
Title: How to analyze co-occurrence of multiple SNPs?
ThreadText: # 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 @username_0 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)
  
  
  ---
  
  