pca selection statistic
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Description
I am having trouble calculating the PCA selection statistics described in Galinsky 2016 Fast PCA paper using the Eigensoft software.
In EIG v6.1.4 there appears to be a parameter file example.pcaselection.par and the output example.pcaselection.chisq but I’m unable to figure out how to run and produce this output. I have been unable to locate information about the selection statistic (pcaselection) in the README files (both in POPGEN and EIGENSOFT). It does say that “pcaselection was omitted from 6.1.3 by accident" but I don’t see any mention of it besides the example output in 6.1.4.
Have the names of this function changed? Could you point me to the explanation of how to run and generate the selection statistics using the pre-computed eigenvectors?
Any help is greatly appreciated,
Rachel Blumhagen
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Research direction
Start by reviewing example.pcaselection.par and example.pcaselection.chisq, then compare the POPGEN and EIGENSOFT README files. Document how to run pcaselection with pre-computed eigenvectors, clarify whether the function names changed, and include the expected output.
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Assessment
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100