<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>

CC BY-SA 4.0
2021-04-09T22:28:51.437Z
https://academic.oup.com/bioinformatics/article/28/19/2537/288671
user438383
CC BY-SA 4.0
2021-04-14T05:20:39.267Z
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
user3479780
<snp><haplotypes><graphs>
How to plot a graph of Linkage disequilibrium with limited information
# 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

