modify load LD plink matrix function

raiss/ld_matrix.py

@@ -74,7 +74,7 @@ def load_plink_ld(plink_ld, ref_chr_df):
     plink_ld = plink_ld + ".ld"
     plink_ld = pd.read_csv(plink_ld, sep = "\s+")
     mat_ld = plink_ld.pivot(index='SNP_A', columns='SNP_B', values='R')
-    un_index = mat_ld.index.union(mat_ld.columns)
+    un_index = mat_ld.index.intersection(mat_ld.columns)
     mat_ld = mat_ld.reindex(index=un_index, columns=un_index)
     mat_ld.fillna(0, inplace=True)
     sym = np.where(np.abs(mat_ld.values) > np.abs(mat_ld.values.transpose()), mat_ld.values, mat_ld.values.transpose())

raiss/stat_models.py

@@ -104,5 +104,6 @@ def raiss_model(zt, sig_t, sig_i_t, lamb=0.01, rcond=0.01,  batch=True):
         var_norm = var_in_boundaries(var, lamb)
 
         R2 = ((1+lamb)-var_norm)
+        print(R2)
         mu = mu / np.sqrt(R2)
         return({"var" : var, "mu" : mu, "ld_score" : ld_score, "condition_number" : condition_number, "correct_inversion":correct_inversion })