admix.cli.genet_cor#

admix.cli.genet_cor(pheno: str, grm_prefix: str, out_dir: str, rg_grid=array([0., 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1.]), quantile_normalize: bool = True, n_thread: int = 2, clean: bool = True)[source]#

Estimate genetic correlation

Parameters:

  • pheno (str) – phenotype file, the 1st column contains ID, 2nd column contains phenotype, and the rest of columns are covariates.

  • grm_prefix (str) – folder containing K1, K2 GRM files

  • out_dir (str) – folder to store the output files

  • rg_grid (list, optional) – List of rg values to grid search, by default np.linspace(0, 1.0, 21)

  • quantile_normalize (bool) – whether to perform quantile normalization for both phenotype and each column of covariates

  • n_thread (int, optional) – number of threads, by default 2