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EvolEcolGroup / tidypopgen

https://evolecolgroup.github.io/tidypopgen/
GNU General Public License v3.0
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Project samples on pca #31

Closed dramanica closed 3 months ago

dramanica commented 4 months ago

We should set up something similar to: https://github.com/ChristianHuber/smartsnp/blob/master/vignettes/aDNA_smartpca_analysis.Rmd

Checking that we can match eigenstrat for PCA. In the process, we could develop a couple of functions to directly read packedancestry files using admixtools2.

dramanica commented 4 months ago

Implemented standard project for samples without missing data in 427c9c016a02a6a79e269003e4f11c050112c588, we just need an example.

dramanica commented 3 months ago

For projecting, we should add the option of replacing the missing data with the mean values from the PCA object.

dramanica commented 3 months ago

Implemented simple projection in #43 . We now need to implement lsq projection as used in smartpca or smartsnp, for samples with lots of missing data.