no smote

Author: pizza6inch

config/prostate.json

@@ -0,0 +1,40 @@
+{
+  "GDC_prostate_tissue": {
+    "normal": 50,
+    "tumor": 502,
+    "sample_count": 2,
+    "sample_type": "tissue",
+    "file": "../prostate/champ_result/GDC_prostate_tissue/all_beta_normalized.csv",
+    "split_test": 0.2,
+    "random_state": 42
+  },
+  "GDC_prostate_tissue_80": {
+    "normal": 40,
+    "tumor": 401,
+    "file": "../prostate/champ_result/GDC_prostate_tissue_80/all_beta_normalized.csv"
+  },
+  "GDC_prostate_tissue_20_test": {
+    "normal": 10,
+    "tumor": 101,
+    "file": "../prostate/champ_result/GDC_prostate_tissue_20_test/all_beta_normalized.csv"
+  },
+  "GSE269244": {
+    "normal": 118,
+    "tumor": 120,
+    "sample_count": 2,
+    "sample_type": "tissue",
+    "file": "../prostate/champ_result/GSE269244/all_beta_normalized.csv",
+    "split_test": 0.2,
+    "random_state": 42
+  },
+  "GSE269244_80": {
+    "normal": 94,
+    "tumor": 96,
+    "file": "../prostate/champ_result/GSE269244_80/all_beta_normalized.csv"
+  },
+  "GSE269244_20_test": {
+    "normal": 24,
+    "tumor": 24,
+    "file": "../prostate/champ_result/GSE269244_20_test/all_beta_normalized.csv"
+  }
+}

config/prostate_plan_A.toml

@@ -0,0 +1,75 @@
+[init.hyper]
+df_file_1 = "../prostate/champ_result/GDC_prostate_tissue_80/all_beta_normalized.csv"
+df_file_2 = "../prostate/champ_result/GSE269244_80/all_beta_normalized.csv"
+dmp_file_1 = "../prostate/champ_result/GDC_prostate_tissue/DMP_result_TN.csv"
+dmp_file_2 = "../prostate/champ_result/GSE269244/DMP_result_TN.csv"
+majority_out_path_1 = "../prostate/planA/GDC_prostate_tissue/split80train"
+majority_out_path_2 = "../prostate/planA/GSE269244/split80train"
+joined_out_path = "../prostate/planA/joined"
+
+[GO_distance_matrix.hyper]
+input_file = "prostate/planA/joined/section_2/dbeta_TSS_threshold_joined.csv"
+base_out_dir = "prostate/planA/joined/GO_distance_matrix"
+
+[clustering_visual.hyper]
+result_prefix = "dbeta_TSS_threshold_joined"
+dbeta_file = "../prostate/planA/joined/section_2/dbeta_TSS_threshold_joined.csv"
+bp_file = "../prostate/planA/joined/GO_distance_matrix/distance_matrix_bp.csv"
+cc_file = "../prostate/planA/joined/GO_distance_matrix/distance_matrix_cc.csv"
+mf_file = "../prostate/planA/joined/GO_distance_matrix/distance_matrix_mf.csv"
+terms_count_file = "../prostate/planA/joined/GO_distance_matrix/terms_count.csv"
+result_out_path = "../prostate/planA/joined/section_5"
+
+[simple_model.hyper]
+dbeta_file = "../prostate/planA/joined/section_5/dbeta_TSS_threshold_joined_consensus.csv"
+selected_feature_file = "../prostate/planA/GDC_prostate_tissue/split80train/section_3/rfe/selected_features.json"
+selected_feature_file_2 = "../prostate/planA/GSE269244/split80train/section_3/rfe/selected_features.json"
+train_out_path = "../prostate/planA/joined/split80train/section_6"
+validate_out_path = "../prostate/planA/joined/split20test/section_6"
+df_train_file = "../prostate/champ_result/GDC_prostate_tissue_80/all_beta_normalized.csv"
+df_test_file = "../prostate/champ_result/GDC_prostate_tissue_20_test/all_beta_normalized.csv"
+df_train_file_2 = "../prostate/champ_result/GSE269244_80/all_beta_normalized.csv"
+df_test_file_2 = "../prostate/champ_result/GSE269244_20_test/all_beta_normalized.csv"
+training_param_file = "../prostate/training_param.json"
+
+[preprocess.filtering]
+threshold_TCGA = 0.36
+threshold_GEO = 0.21
+
+[preprocess.dbeta]
+delta_beta_avg_feature_numTCGA = 373340
+NaN_dbeta_featureTCGA = []
+delta_beta_avg_feature_num_remove_NaNTCGA = 373340
+dmp_before_dropna_shape_featureTCGA = 286098
+dmp_after_dropna_shape_featureTCGA = 218741
+delta_beta_avg_feature_num_remove_NaN_join_dmpTCGA = 373340
+delta_beta_avg_feature_numGEO = 695602
+NaN_dbeta_featureGEO = []
+delta_beta_avg_feature_num_remove_NaNGEO = 695602
+dmp_before_dropna_shape_featureGEO = 188706
+dmp_after_dropna_shape_featureGEO = 136630
+delta_beta_avg_feature_num_remove_NaN_join_dmpGEO = 695602
+
+[preprocess.filtering.hyper]
+avg_dbeta_lower_bound = 300
+avg_dbeta_upper_bound = 500
+
+[feature_selection.rfe.hyper]
+train_out_path = "../prostate/planA/GDC_prostate_tissue/split80train/section_3/rfe"
+dbeta_info_file = "../prostate/planA/joined/section_5/dbeta_TSS_threshold_joined_consensus.csv"
+training_param_file = "../prostate/training_param.json"
+
+[feature_selection.sfs.hyper]
+train_out_path = "../prostate/planA/GDC_prostate_tissue/split80train/section_3/sfs"
+dbeta_info_file = "../prostate/planA/joined/section_5/dbeta_TSS_threshold_joined_consensus.csv"
+training_param_file = "../prostate/training_param.json"
+
+[feature_selection_2.rfe.hyper]
+train_out_path = "../prostate/planA/GSE269244/split80train/section_3/rfe"
+dbeta_info_file = "../prostate/planA/joined/section_5/dbeta_TSS_threshold_joined_consensus.csv"
+training_param_file = "../prostate/training_param.json"
+
+[feature_selection_2.sfs.hyper]
+train_out_path = "../prostate/planA/GSE269244/split80train/section_3/sfs"
+dbeta_info_file = "../prostate/planA/joined/section_5/dbeta_TSS_threshold_joined_consensus.csv"
+training_param_file = "../prostate/training_param.json"