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One more thing - it was discussed at lab meeting that instead of `Ambiguous`, it should say `Other` in the labels that `predictEthnicity` outputs, since the tool can only calculate 3 ancestries but there are other ancestries out there (+ ancestry is a continuum) so in reality samples being called ambiguous may just be mixed or from an ancestry other than African/Asian/European. Let me know what you think and if you agree I'm happy to change that myself too!
Hey Iciar, so the "amibguous" class is for samples with uncertain predictions, where "uncertain" is defined at some probability cutoff (75% as default). In my paper I show these samples below this threshold to correlate well with mixed genetic ancestry of the three reference ancestries. Because of this, I think "ambiguous" would be better changed to something like "mixed" .
The ethnicity predictor has no way of telling if the queried data is not any of the 3 ancestries used in training data, so I think calling it "other" would be too assumptive and sometimes just wrong.
Originally posted by @iciarfernandez in #19 (comment)
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