Answers.Body: <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>
  
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Answers.Text: 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.
Answers.UserDisplayName: user2887
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Answers.Text: @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.
Answers.UserDisplayName: Kamil S Jaron
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Answers.CreationDate: 2018-06-03T17:46:19.327Z
Answers.Text: 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".
Answers.UserDisplayName: Kamil S Jaron
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Answers.LastEditDate: 2018-06-03T21:27:05.140Z
Answers.UserDisplayName: Kamil S Jaron
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-03T21:30:33.260Z
Comments.Text: 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?
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-13T00:52:13.003Z
Comments.Text: What is the question?
Comments.UserDisplayName: winni2k
Tags: <snp><phylogenetics><snp-chip>
Title: Statistical approach to compare the SNP genotyping data among set of individuals
ThreadText: # 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?  
  
  ---
  
  ## 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**: @username_0 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".  
  
  ---
  
  