<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>

CC BY-SA 4.0
2020-04-22T02:50:41.910Z
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
Amara
CC BY-SA 4.0
2020-04-20T12:26:25.167Z
2020-04-20T12:26:25.167Z
zhanxw
<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>

<bioconductor><plink>
How to calculate average minor allele frequency (MAF) difference between two populations (i.e. European, Hispanic)
# 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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