Hi,
I’m trying to use Hail to run a logistic regression GWAS on a case-control(0 vs 1) phenotype. I have two questions:
- What input phenotype is expected by Hail? 0 vs 1 in tfloat64 format or True vs False in tbool format?
- If I would like to run Hail in .py scripts on remote school linux servers, are there any mistakes I made in my code?
#!/s/bin/python3
import hail as hl
hl.init()mt = hl.import_plink(bed=‘chr22.bed’,bim=‘chr22.bim’,fam=‘chr22.fam’,quant_pheno=False)
covar = (hl.import_table(‘pheno_covariate.txt’,types={‘IID’:hl.tstr,‘mypheno’:hl.tbool},impute=True).key_by(‘IID’))mt = mt.annotate_cols(covar=covar[mt.s])
mt_logistic =hl.logistic_regression_rows(test=‘wald’,y=[mt.covar.mypheno,mt.covar.mypheno],x=mt.GT.n_alt_alleles(),
covariates=[1,mt.covar.IsMale,mt.covar.Year,mt.covar.IsAxiom,mt.covar.PC1,mt.covar.PC2,
mt.covar.PC3,mt.covar.PC4,mt.covar.PC5,mt.covar.PC6,mt.covar.PC7,
mt.covar.PC8,mt.covar.PC9,mt.covar.PC10])mt_logistic.export(‘chr22_hail.txt’)