<p>PCA sounds like a good start to see a rough population structure among your 96 individuals, this step is half a sane thing to do, but also it can give you a hint how many distinct populations there are in your dataset. I have not personally run PCA on SNP data, but it seems that there are quite lot of tutorials online. For instance <a href="https://privefl.github.io/bigsnpr/articles/how-to-PCA.html" rel="nofollow noreferrer">this one</a> looks  nice.</p>

<p>Once you know how many categories you can expect in your population, you can use <a href="https://web.stanford.edu/group/pritchardlab/structure.html" rel="nofollow noreferrer">Structure</a> to classify individuals to the categories.</p>

CC BY-SA 4.0
2018-06-03T15:27:43.777Z
Sorry if I wasn't able to make it clear, but ya that's precisely what I want to do. I want to see if the individuals cluster in any manner whatsoever. Did you mean PCA by any chance in your answer? So exactly how would I go about doing it. I know what PCA does in theory but I am not able to understand how I can create a PCA plot with the data I have in hand.
user2887
CC BY-SA 4.0
2018-06-03T17:40:38.367Z
@user2887 Oh, yes. I meant PCA, fixed that already. Note that you can also edit your question, to make it clearer or to add more details.
Kamil S Jaron
CC BY-SA 4.0
2018-06-03T17:46:19.327Z
Hey, I edited the answer (added a link to a blogpost where they show how to do PCA on SNP data). Seems that quite lot of them out there if you google "pca genotype data".
Kamil S Jaron
CC BY-SA 4.0
2018-06-03T13:52:45.647Z
2018-06-03T21:27:05.140Z
2018-06-03T21:27:05.140Z
Kamil S Jaron
<p>So, I have the genotyping data of about 650,000 SNPs for 96 individuals. I already know the Y DNA haplogroup of these individuals, so to some extent, I have a gross understanding of their ancestry. </p>

<p>What would be the best way to go about doing this? From what I have been reading, maybe a PCA would be a good idea? Suppose individuals 1-10 belong to a particular population (unique ancestary) then their SNP genotypes should be significantly similar to each other than say individuals 11-20 who belong to another population group. So, in theory I should get two clusters in my PCA plot.</p>

<p>I have the genotype of each SNP for each individual. How would I go about creating a PCA plot or any other alternative way of analysis for this kind of questions. </p>

CC BY-SA 4.0
2018-06-03T21:30:33.260Z
Way better. Now one of your question is, "how to make a PCA plot". There are the plenty of tutorials out there, have you tried one? Yes? What what was the problem with it?
Kamil S Jaron
CC BY-SA 4.0
2018-06-13T00:52:13.003Z
What is the question?
winni2k
<snp><phylogenetics><snp-chip>
Statistical approach to compare the SNP genotyping data among set of individuals
# Statistical approach to compare the SNP genotyping data among set of individuals

(Asked by: username_0 on 2018-06-02)

So, I have the genotyping data of about 650,000 SNPs for 96 individuals. I already know the Y DNA haplogroup of these individuals, so to some extent, I have a gross understanding of their ancestry.

What would be the best way to go about doing this? From what I have been reading, maybe a PCA would be a good idea? Suppose individuals 1-10 belong to a particular population (unique ancestary) then their SNP genotypes should be significantly similar to each other than say individuals 11-20 who belong to another population group. So, in theory I should get two clusters in my PCA plot.

I have the genotype of each SNP for each individual. How would I go about creating a PCA plot or any other alternative way of analysis for this kind of questions.

**Tags:** snp, phylogenetics, snp-chip
> **Comments:**
> **username_1**: Way better. Now one of your question is, "how to make a PCA plot". There are the plenty of tutorials out there, have you tried one? Yes? What what was the problem with it?  
> **username_2**: What is the question?  

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## 1 answers

### Answer by username_1 on 2018-06-03. Score: 3 | Accepted answer

PCA sounds like a good start to see a rough population structure among your 96 individuals, this step is half a sane thing to do, but also it can give you a hint how many distinct populations there are in your dataset. I have not personally run PCA on SNP data, but it seems that there are quite lot of tutorials online. For instance [this one](https://privefl.github.io/bigsnpr/articles/how-to-PCA.html) looks nice.

Once you know how many categories you can expect in your population, you can use [Structure](https://web.stanford.edu/group/pritchardlab/structure.html) to classify individuals to the categories.

> **Comments:**
> **username_0**: Sorry if I wasn't able to make it clear, but ya that's precisely what I want to do. I want to see if the individuals cluster in any manner whatsoever. Did you mean PCA by any chance in your answer? So exactly how would I go about doing it. I know what PCA does in theory but I am not able to understand how I can create a PCA plot with the data I have in hand.  
> **username_1**: @user2887 Oh, yes. I meant PCA, fixed that already. Note that you can also edit your question, to make it clearer or to add more details.  
> **username_1**: Hey, I edited the answer (added a link to a blogpost where they show how to do PCA on SNP data). Seems that quite lot of them out there if you google "pca genotype data".  

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