Hi, I am new to hail and trying to implement binary trait in hail. The set up is 1, The phenotype is in 1, 0 format 2, I imported plink file using hl.import_plink and set quant_pheno= False and set it to mt 3, I imported covariate using hl.import_table and use annotate_cols to incorporate covar…

Hey @fengyi , I’m sorry you’re having trouble! In the future, if you share the exact code you ran, we can more easily help you. It is also easier to help you when you copy and paste the exact output you get (like the is_case column). As to your questions: You specified that your trait is not a qu…

Hi @danking , thank you for your help! I have imported it as quantitative phenotype and it seems like it automatically set 0 to -9. when I tried mt = mt.annotate_columns(is_case = hl.bool(mt.quant_pheno)) [Screen Shot 2020-09-23 at 10.49.03 AM] It seems like everything became true. Do you know h…

You’re looking for case mt.annotate_columns(is_case = hl.case() .when(mt.quant_pheno == -9, False) .when(mt.quant_pheno == 1, True) .or_missing())

Logistic regression implementation

Hail Query & hailctl

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Logistic regression implementation

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