Update imputation_R2.py

raiss/imputation_R2.py

@@ -143,7 +143,7 @@ def grid_search(zscore_folder, masked_folder, output_folder,
                 eigen_ratio_grid = [0.5, 0.1, 0.01], window_size= 500000,
                  buffer_size=125000, l2_regularization=0.1, R2_threshold=0.6,
                  N_to_mask=5000,ref_panel_suffix=".eur.1pct.bim", ld_type="plink",
-                 stratifying_vector=None, stratifying_bins=None):
+                 stratifying_vector=None, stratifying_bins=None, LD_threshold=4):
     """
     Compute the imputation performance for several eigen ratioself.
     The procedure is the following:
@@ -184,7 +184,7 @@ def grid_search(zscore_folder, masked_folder, output_folder,
         save_chromosome_imputation(gwas, chrom, window_size, buffer_size,
                                    l2_regularization, cond, masked_folder,
                                    ref_folder, ld_folder, output_folder,
-                                 R2_threshold, tag, ref_panel_suffix, ld_type)
+                                 R2_threshold, tag, ref_panel_suffix, ld_type, minimum_ld = LD_threshold)
 
     n_cpu = multiprocessing.cpu_count()
     Parallel(n_jobs=n_cpu)(delayed(run_imputation)(rd) for rd in eigen_ratio_grid)