Answers.Body: <ol>
  <li>You need to report allele frequencies using <code>plink</code> for some European samples</li>
  <li>Do the same for Hispanic samples</li>
  <li>Use a software to subtract the two allele frequencies obtained above and obtain the result.</li>
  </ol>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-22T02:50:41.910Z
Answers.Text: Hi, I think I kind of understood what you mean. So in PLINK, we use --freq command to find information on frequency. and what software do you recommend to subtract the frequency files of two populations? thank You
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Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-20T12:26:25.167Z
Answers.LastActivityDate: 2020-04-20T12:26:25.167Z
Answers.UserDisplayName: zhanxw
Body: <p>The data is present in the PLINK format .bed (individual genotypes), .bim (genetic markers) and .fam (sample IDs and disease phenotype file). I have also separate text files containing information on subjects related to two populations. (i.e. European and Hispanic)</p>
  
  <p><a href="https://i.sstatic.net/NDGdV.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/NDGdV.png" alt="Question related PLINK data"></a></p>
  
Tags: <bioconductor><plink>
Title: How to calculate average minor allele frequency (MAF) difference between two populations (i.e. European, Hispanic)
ThreadText: # How to calculate average minor allele frequency (MAF) difference between two populations (i.e. European, Hispanic)
  
  (Asked by: username_0 on 2020-04-18)
  
  The data is present in the PLINK format .bed (individual genotypes), .bim (genetic markers) and .fam (sample IDs and disease phenotype file). I have also separate text files containing information on subjects related to two populations. (i.e. European and Hispanic)
  
  [![Question related PLINK data](https://i.sstatic.net/NDGdV.png)](https://i.sstatic.net/NDGdV.png)
  
  **Tags:** bioconductor, plink
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2020-04-20. Score: 1
  
  1. You need to report allele frequencies using `plink` for some European samples
  2. Do the same for Hispanic samples
  3. Use a software to subtract the two allele frequencies obtained above and obtain the result.
  
  > **Comments:**
  > **username_0**: Hi, I think I kind of understood what you mean. So in PLINK, we use --freq command to find information on frequency. and what software do you recommend to subtract the frequency files of two populations? thank You  
  
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