Eigenstrat for 3 subpopulations
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Description
Hi
I have a list of SNPs from 3 subpopulations pairwise association tests (1vs2 ,2vs3, 1vs3) that i need to check for population stratification.I have PC1-10 values for all the 3 subpopulations taken together.
However,in eigenstrat we have to define case-control to samples for chi-square test which in my case i have only for 2 subpopulations at a time.
Is it technically correct to take PC1-10 for 2 subgroups at a time and do the correction using eigenstrat?
Kindly suggest
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Research direction
The issue names no source file, test, or entry point. Start by reviewing the Eigenstrat workflow for case-control inputs and principal components across multiple subpopulations. Done means providing a maintainer-confirmed answer about whether the combined PC1–10 values are valid for each pairwise correction.
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Assessment
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 15/100