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 covariates to the mt
4, last I did something like, gwas =hl.logistic_regression_rows(test=‘wald’,
y=[mt.is_case, mt.is_case],
x=mt.GT.n_alt_alleles()
, covariates= [1, mt.covar.1, mt.covar.2, …])
Question:
1, Why is my is case in bool format?
2, Can you also help me to understand this error? Error summary: HailException: For logistic regression, y at index 0 must be non-constant
3, I am not sure if I am implementing logistic regression correctly, can you let me know if there is anything I should change?
Thank you!
-Fengyi