smartpca eigen vector file missing individuals
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- Dominant language
- C
- Stars
- 207
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- 61
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Description
Hello,
I noticed that I am missing some individuals in my eigen vector output file after running smartpca. My total number of individuals is 322 and the file only has information for 300 individuals. Is there some form of filtering that is done by the software that I am not accounting for?
I also checked the .ind file to see if some may have been mis-assigned to a population with a typo but that doesn't seem to be the case. I would greatly appreciate your help.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the smartpca run described in the issue and compare the 322 individuals with the 300 entries in the eigenvector output. Investigate whether smartpca filters individuals despite the reported .ind population assignments; done means explaining the discrepancy or identifying a reproducible software defect.
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Assessment
- Tech stack
- c
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100