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Atkinson-Lab / Tractor

Scripts for implementing the Tractor pipeline
MIT License
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NaN output #13

Closed spaul-genetics closed 10 months ago

spaul-genetics commented 2 years ago

I am applying the pipeline on imputed data (chr 21) of 934 cases and 946 controls. The output I got contains all nan. Is it possibly due to the small sample size?

JasonTan-code commented 2 years ago

This could happen if one of your dosage file contains all 0s, and if that happens, the program can’t fit a linear/logistic regression. Have you checked the global proportions of admixture? If this is the problem, you may need to consider reducing the number of local ancestries call (for example, from 3-way LAI to 2-way LAI).

nirav572 commented 10 months ago

Closing this issue due to prolonged inactivity.