Body: <p>I have a snp information in an excel file and I used SNPstat to do some analysis. But I also need a plot of LD for these snps. But my file is not formatted as the most programs required (.ped, hapmap, Plink...). Here is a screen shot of file: <a href="https://i.sstatic.net/6Vja9.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/6Vja9.png" alt="Data file" /></a></p>
  <p>I have also chromosome numbers and rs information for this snps. Due to this data format problem I couldn't use Haploview or other programs. Can you suggest me a solution to create a LD graph?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-04-09T22:28:51.437Z
Comments.Text: https://academic.oup.com/bioinformatics/article/28/19/2537/288671
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-04-14T05:20:39.267Z
Comments.Text: you need an LD matrix, which your table is not.  The LD matrix is a pairwise matrix.  See this page for an example: https://www.rdocumentation.org/packages/gaston/versions/1.4.9/topics/LD.plot
Comments.UserDisplayName: user3479780
Tags: <snp><haplotypes><graphs>
Title: How to plot a graph of Linkage disequilibrium with limited information
ThreadText: # How to plot a graph of Linkage disequilibrium with limited information
  
  (Asked by: username_0 on 2021-04-09)
  
  I have a snp information in an excel file and I used SNPstat to do some analysis. But I also need a plot of LD for these snps. But my file is not formatted as the most programs required (.ped, hapmap, Plink...). Here is a screen shot of file: [![Data file](https://i.sstatic.net/6Vja9.png)](https://i.sstatic.net/6Vja9.png)
  
  I have also chromosome numbers and rs information for this snps. Due to this data format problem I couldn't use Haploview or other programs. Can you suggest me a solution to create a LD graph?
  
  **Tags:** snp, haplotypes, graphs
  
  > **Comments:**
  > **username_1**: https://academic.oup.com/bioinformatics/article/28/19/2537/288671  
  > **username_2**: you need an LD matrix, which your table is not.  The LD matrix is a pairwise matrix.  See this page for an example: https://www.rdocumentation.org/packages/gaston/versions/1.4.9/topics/LD.plot  
  
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  ## 0 answers
  
  