various panel updates

.gitignore

@@ -11,4 +11,5 @@
 **/*tar.gz
 **/*tar
 **/*gz
-clustering_runs/*/*
+clustering_runs/*/*
+data_tables/maf_files/*

data_tables/confusion_matrices/NN_no.sv_no.arms_reducedV3.4_removeN5_nfeatures18.txt

@@ -0,0 +1,49 @@
+Format: TRUE labels in ROWS, PREDICTED labels in COLUMNS
+Confusion Matrix All
+   92	  3	  4	  9	  6 
+    1	110	  4	  4	  8 
+    4	  7	 71	  4	  9 
+    4	  1	  4	 59	  7 
+    4	  3	  3	  3	126  
+Overall Accuracy: 0.8327272727272728
+Confusion Matrix Top 70%
+   75	  2	  0	  0	  4 
+    0	 91	  0	  0	  3 
+    2	  3	 56	  0	  2 
+    1	  0	  0	 39	  2 
+    0	  0	  0	  0	105  
+Accuracy Top 70%: 0.9506493506493506
+Confusion Matrix Above 0.90
+  45	 1	 0	 1 
+   0	68	 0	 1 
+   0	 1	31	 1 
+   0	 0	 0	70  
+Accuracy Above 0.90: 0.9771689497716894
+Confusion Matrix 0.80_0.90
+  19	 0	 0	 0	 2 
+   0	14	 0	 0	 1 
+   1	 1	13	 0	 0 
+   1	 0	 0	25	 1 
+   0	 0	 0	 0	22  
+Accuracy 0.80 < Conf <= 0.90: 0.93
+Confusion Matrix 0.70_0.80
+   9	 0	 0	 0	 1 
+   0	 7	 0	 0	 1 
+   1	 0	12	 0	 1 
+   0	 0	 0	13	 1 
+   0	 0	 0	 0	10  
+Accuracy 0.70 < Conf <= 0.80: 0.9107142857142857
+Confusion Matrix <= 0.70
+  19	 2	 4	 9	 2 
+   1	21	 4	 4	 5 
+   2	 5	15	 4	 7 
+   3	 1	 4	21	 5 
+   4	 3	 3	 3	24  
+Accuracy Conf <= 0.70: 0.5714285714285714
+Confusion Matrix > 0.70
+   73	  1	  0	  0	  4 
+    0	 89	  0	  0	  3 
+    2	  2	 56	  0	  2 
+    1	  0	  0	 38	  2 
+    0	  0	  0	  0	102  
+Accuracy Conf > 0.70: 0.9546666666666667

data_tables/confusion_matrices/staudt_subsets/confusionmatrices_staudt_subsets_confusionmatrices.txt

@@ -0,0 +1,49 @@
+Format: TRUE labels in ROWS, PREDICTED labels in COLUMNS
+staudt_ours_test_n=65
+  10	 0	 0	 3	 0 
+   0	20	 0	 1	 1 
+   0	 0	 9	 0	 0 
+   0	 0	 0	 9	 1 
+   0	 0	 0	 0	11  
+accuracy: 0.9076923076923077
+
+staudt_raw_test_n=65
+  11	 0	 0	 1	 1 
+   0	21	 0	 0	 1 
+   0	 0	 9	 0	 0 
+   0	 0	 0	 9	 1 
+   0	 0	 0	 0	11  
+accuracy: 0.9384615384615385
+
+staudt_ours_train_n=357
+  82	 1	 1	 0	 2 
+   0	67	 0	 1	 2 
+   0	 1	50	 1	 1 
+   2	 0	 2	44	 2 
+   1	 1	 2	 1	93  
+accuracy: 0.9411764705882353
+
+staudt_raw_train_n=357
+  72	 2	 5	 5	 2 
+   0	63	 1	 1	 5 
+   2	 2	46	 3	 0 
+   3	 4	 3	37	 3 
+   0	 3	 2	 0	93  
+accuracy: 0.8711484593837535
+
+staudt_ours_all_n=422
+   92	  1	  1	  3	  2 
+    0	 87	  0	  2	  3 
+    0	  1	 59	  1	  1 
+    2	  0	  2	 53	  3 
+    1	  1	  2	  1	104  
+accuracy: 0.9360189573459715
+
+staudt_raw_all_n=422
+   83	  2	  5	  6	  3 
+    0	 84	  1	  1	  6 
+    2	  2	 55	  3	  0 
+    3	  4	  3	 46	  4 
+    0	  3	  2	  0	104  
+accuracy: 0.8815165876777251
+

data_tables/confusion_matrices/test_set/confusionmatrices_no.arms_no.sv.txt

@@ -0,0 +1,43 @@
+Format: TRUE labels in ROWS, PREDICTED labels in COLUMNS
+Confusion Matrix All
+  14	 0	 4	 8	 0 
+   1	31	 1	 7	 4 
+   1	 1	19	 1	 0 
+   1	 0	 0	20	 1 
+   2	 2	 4	 0	27  
+Overall Accuracy: 0.7449664429530202
+Confusion Matrix Top 70%
+  14	 0	 0	 3	 0 
+   0	24	 0	 0	 2 
+   0	 0	17	 0	 0 
+   0	 0	 0	18	 0 
+   2	 0	 1	 0	24  
+Accuracy Top 70%: 0.9238095238095239
+Confusion Matrix Above 0.90
+   5	 0	 0	 1	 0 
+   0	15	 0	 0	 0 
+   0	 0	10	 0	 0 
+   0	 0	 0	 2	 0 
+   0	 0	 0	 0	10  
+Accuracy Above 0.90: 0.9767441860465116
+Confusion Matrix 0.80_0.90
+   6	 0	 0	 0	 0 
+   0	 3	 0	 0	 0 
+   0	 0	 5	 0	 0 
+   0	 0	 0	12	 0 
+   0	 0	 0	 0	 6  
+Accuracy 0.80 < Conf <= 0.90: 1.0
+Confusion Matrix 0.70_0.80
+  3	0	0	2	0 
+  0	5	0	0	0 
+  0	0	2	0	0 
+  0	0	0	4	0 
+  0	0	0	0	5  
+Accuracy 0.70 < Conf <= 0.80: 0.9047619047619048
+Confusion Matrix <= 0.70
+  0	0	4	5	0 
+  1	8	1	7	4 
+  1	1	2	1	0 
+  1	0	0	2	1 
+  2	2	4	0	6  
+Accuracy Conf <= 0.70: 0.33962264150943394