search

AI-sandbox / XGMix

13 stars 2 forks source link

doubts about the config.py #11

Closed vicbp1 closed 3 years ago

vicbp1 commented 3 years ago

Hi all, My doubts about the config.py file is about the generations flag. If I know that the admixture event between my target population was during the last 10 generations, do I have to reduce From: generations = [0, 2, 4, 6, 8, 12, 16, 24, 32, 48] To: generations = [0, 2, 4, 6, 8, 12] or generations = [0, 2, 4, 6, 8, 12, 16]

Or this parameter will not affect the inference? One last doubt is how deep in time does xgmix can infer local ancestry? I mean 50 or more generations ago? (Considering that we have proxies for the admixture event)

Thank you in advance!

weekend37 commented 3 years ago

Hey there! The short answer is that it's not critical in terms of performance. However it does affect inference somewhat and if you're certain about your time since admixture, I would recommend changing it like you said!

This model is able to infer ancestries in very high generations including more than 50, yes. It obviously performs a bit worse than for the lower generation regime as the inference problem is getting harder but it still does quite well.