[1] "ofn"        "-oTCESC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CESC-TP/19775059/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/19779738/transformed.cor.cli.txt"

nPatients in clinical file=307, in cluster file=295, common to both=295
[1]  82 295
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               90               205 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               90               205 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              140               155 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              140               155 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               64               231 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               64               231 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               37               258 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               37               258 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               71               224 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               71               224 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              175               120 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              175               120 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               284 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               284 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               279 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               16               279 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              113               182 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              113               182 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               44               251 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               44               251 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               52               243 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               52               243 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               36               259 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               36               259 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               38               257 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               38               257 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               37               258 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               37               258 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               53               242 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               53               242 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               91               204 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               91               204 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               49               246 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               49               246 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               47               248 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               47               248 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                25                270 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                25                270 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                17                278 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                17                278 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                286 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                286 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                287 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                287 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                53                242 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                53                242 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                50                245 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                50                245 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                24                271 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                24                271 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                47                248 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                47                248 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                52                243 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                52                243 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                44                251 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                44                251 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                40                255 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                40                255 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                273 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                273 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                42                253 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                42                253 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                49                246 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                49                246 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                32                263 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                32                263 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                44                251 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                44                251 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                72                223 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                72                223 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               100                195 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               100                195 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               115                180 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               115                180 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                37                258 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                37                258 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                29                266 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                29                266 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               42               253 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               42               253 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               42               253 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               42               253 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               282 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               282 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               286 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               286 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               19               276 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               19               276 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               35               260 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               35               260 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               82               213 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               82               213 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               14               281 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               14               281 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              131               164 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              131               164 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               93               202 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               93               202 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               19               276 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               19               276 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               51               244 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               51               244 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               47               248 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               47               248 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               74               221 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               74               221 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               26               269 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               26               269 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               37               258 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               37               258 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               82               213 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               82               213 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               24               271 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               24               271 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               54               241 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               54               241 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               51               244 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               51               244 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                66                229 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                66                229 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                74                221 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                74                221 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               100                195 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               100                195 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               115                180 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               115                180 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                40                255 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                40                255 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                280 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                280 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                80                215 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                80                215 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                260 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                260 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                47                248 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                47                248 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                34                261 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                34                261 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                44                251 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                44                251 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                95                200 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                95                200 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                37                258 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                37                258 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                55                240 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                55                240 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                73                222 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                73                222 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                60                235 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                60                235 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                29                266 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                29                266 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                23                272 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                23                272 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                285 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                285 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                49                246 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                49                246 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                71                224 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                71                224 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               63               232 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               63               232 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               59               236 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               59               236 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                          
 [2] "VITAL_STATUS"                            
 [3] "DAYS_TO_DEATH"                           
 [4] "DAYS_TO_LAST_FOLLOWUP"                   
 [5] "TUMOR_TISSUE_SITE"                       
 [6] "PATHOLOGIC_STAGE"                        
 [7] "PATHOLOGY_T_STAGE"                       
 [8] "PATHOLOGY_N_STAGE"                       
 [9] "PATHOLOGY_M_STAGE"                       
[10] "GENDER"                                  
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"    
[12] "RADIATION_THERAPY"                       
[13] "HISTOLOGICAL_TYPE"                       
[14] "NUMBER_PACK_YEARS_SMOKED"                
[15] "NUMBER_OF_LYMPH_NODES"                   
[16] "RACE"                                    
[17] "ETHNICITY"                               
[18] "WEIGHT_KG_AT_DIAGNOSIS"                  
[19] "TUMOR_STATUS"                            
[20] "NEOPLASM_HISTOLOGIC_GRADE"               
[21] "TOBACCO_SMOKING_YEAR_STOPPED"            
[22] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"       
[23] "TOBACCO_SMOKING_HISTORY"                 
[24] "AGEBEGANSMOKINGINYEARS"                  
[25] "RADIATION_THERAPY_STATUS"                
[26] "PREGNANCIES_COUNT_TOTAL"                 
[27] "PREGNANCIES_COUNT_STILLBIRTH"            
[28] "PREGNANCY_SPONTANEOUS_ABORTION_COUNT"    
[29] "PREGNANCIES_COUNT_LIVE_BIRTH"            
[30] "PREGNANCY_THERAPEUTIC_ABORTION_COUNT"    
[31] "PREGNANCIES_COUNT_ECTOPIC"               
[32] "CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT"
[33] "LYMPH_NODE_LOCATION"                     
[34] "POS_LYMPH_NODE_LOCATION"                 
[35] "MENOPAUSE_STATUS"                        
[36] "LYMPHOVASCULAR_INVOLVEMENT"              
[37] "LYMPH_NODES_EXAMINED_HE_COUNT"           
[38] "LYMPH_NODES_EXAMINED"                    
[39] "KERATINIZATION_SQUAMOUS_CELL"            
[40] "INITIAL_PATHOLOGIC_DX_YEAR"              
[41] "HYSTERECTOMY_TYPE"                       
[42] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"     
[43] "HEIGHT_CM_AT_DIAGNOSIS"                  
[44] "CORPUS_INVOLVEMENT"                      
[45] "CHEMO_CONCURRENT_TYPE"                   
[46] "CERVIX_SUV_RESULTS"                      
[47] "CAUSE_OF_DEATH"                          
[48] "AGE_AT_DIAGNOSIS"                        
[49] "CLINICAL_STAGE"                          

Input Data has 49 rows and 295 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=67,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=203,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'NEOPLASM_HISTOLOGIC_GRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'AGEBEGANSMOKINGINYEARS':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'PREGNANCY_SPONTANEOUS_ABORTION_COUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 29:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 30:'PREGNANCY_THERAPEUTIC_ABORTION_COUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 31:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 32:'CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CERVICAL_CARCINOMA_PELVIC_EXTENSION_TEXT excluded in the analysis because there is no case of (both >= 3) in the table below"
              BILATERAL PELVIC WALL INVOLVEMENT ON IMAGING
freq.values   "1"                                         
freq.contrast "10"                                        
both >= 3     "FALSE"                                     
              CARCINOMA INVOLVES ALL SECTIONS OF THE CERVIX WITH DIRECT EXTENSION INTO THE MYOMETRIAL WALL, PARAMETRIAL TISSUES AND UPPER VAGINA.
freq.values   "1"                                                                                                                                
freq.contrast "10"                                                                                                                               
both >= 3     "FALSE"                                                                                                                            
              METASTASES TO RIGHT OVARY NEGATIVE NO EXTENSION NO PELVIC SPREAD
freq.values   "1"                       "2"      "1"          "1"             
freq.contrast "10"                      "9"      "10"         "10"            
both >= 3     "FALSE"                   "FALSE"  "FALSE"      "FALSE"         
              PELVIC SPREAD
freq.values   "1"          
freq.contrast "10"         
both >= 3     "FALSE"      
              SEVERE SQUAMOUS DYSPLASIA (CIN3) EXTENDING TO THE VAGINAL MARGIN OF EXCISION
freq.values   "1"                                                                         
freq.contrast "10"                                                                        
both >= 3     "FALSE"                                                                     
              THE PELVIC NODULES SHOW CIRCUMSCRIBED AREA OF ADIPOSE TISSUE WITH LOCAL FAT NECROSIS. NO EVIDENCE OF MALIGNANCY WITHIN THIS PELVIC NODULE.
freq.values   "1"                                                                                                                                       
freq.contrast "10"                                                                                                                                      
both >= 3     "FALSE"                                                                                                                                   
              TUMOR EXTENDS 1.0CM INTO 1.3 CM THICK CERVICAL/LOWER UTERINE SEGMENT WALL
freq.values   "1"                                                                      
freq.contrast "10"                                                                     
both >= 3     "FALSE"                                                                  
Variable 33:'LYMPH_NODE_LOCATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "LYMPH_NODE_LOCATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 34:'POS_LYMPH_NODE_LOCATION':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 35:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 36:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 37:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'LYMPH_NODES_EXAMINED':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 39:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 40:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 41:'HYSTERECTOMY_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HYSTERECTOMY_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 42:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 44:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 45:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 46:'CERVIX_SUV_RESULTS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'CAUSE_OF_DEATH':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "CAUSE_OF_DEATH excluded in the analysis because there is no case of (both >= 3) in the table below"
              CARDIOPULMONARY ARREST LUNG CANCER RENAL FAILURE
freq.values   "1"                    "1"         "1"          
freq.contrast "2"                    "2"         "2"          
both >= 3     "FALSE"                "FALSE"     "FALSE"      
Variable 48:'AGE_AT_DIAGNOSIS':	nDistinctValues=61,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 49:'CLINICAL_STAGE':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 295 columns, 1 survival variables, and 38 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                      
 [2] "PATHOLOGY_T_STAGE"                   
 [3] "PATHOLOGY_N_STAGE"                   
 [4] "PATHOLOGY_M_STAGE"                   
 [5] "RADIATION_THERAPY"                   
 [6] "HISTOLOGICAL_TYPE"                   
 [7] "NUMBER_PACK_YEARS_SMOKED"            
 [8] "NUMBER_OF_LYMPH_NODES"               
 [9] "RACE"                                
[10] "ETHNICITY"                           
[11] "WEIGHT_KG_AT_DIAGNOSIS"              
[12] "TUMOR_STATUS"                        
[13] "NEOPLASM_HISTOLOGIC_GRADE"           
[14] "TOBACCO_SMOKING_YEAR_STOPPED"        
[15] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"   
[16] "TOBACCO_SMOKING_HISTORY"             
[17] "AGEBEGANSMOKINGINYEARS"              
[18] "RADIATION_THERAPY_STATUS"            
[19] "PREGNANCIES_COUNT_TOTAL"             
[20] "PREGNANCIES_COUNT_STILLBIRTH"        
[21] "PREGNANCY_SPONTANEOUS_ABORTION_COUNT"
[22] "PREGNANCIES_COUNT_LIVE_BIRTH"        
[23] "PREGNANCY_THERAPEUTIC_ABORTION_COUNT"
[24] "PREGNANCIES_COUNT_ECTOPIC"           
[25] "POS_LYMPH_NODE_LOCATION"             
[26] "MENOPAUSE_STATUS"                    
[27] "LYMPHOVASCULAR_INVOLVEMENT"          
[28] "LYMPH_NODES_EXAMINED_HE_COUNT"       
[29] "LYMPH_NODES_EXAMINED"                
[30] "KERATINIZATION_SQUAMOUS_CELL"        
[31] "INITIAL_PATHOLOGIC_DX_YEAR"          
[32] "HISTORY_HORMONAL_CONTRACEPTIVES_USE" 
[33] "HEIGHT_CM_AT_DIAGNOSIS"              
[34] "CORPUS_INVOLVEMENT"                  
[35] "CHEMO_CONCURRENT_TYPE"               
[36] "CERVIX_SUV_RESULTS"                  
[37] "AGE_AT_DIAGNOSIS"                    
[38] "CLINICAL_STAGE"                      
YEARS_TO_BIRTH, nv=61, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
135  70  21   8 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
135  70  21   8 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
135  70  21   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
135  70  21   8 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=44, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE
WEIGHT_KG_AT_DIAGNOSIS, nv=73, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
NEOPLASM_HISTOLOGIC_GRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=22, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=44, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=FALSE
AGEBEGANSMOKINGINYEARS, nv=28, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_STATUS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=15, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PREGNANCY_SPONTANEOUS_ABORTION_COUNT, nv=7, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=12, binary=FALSE, numeric=TRUE
PREGNANCY_THERAPEUTIC_ABORTION_COUNT, nv=7, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
POS_LYMPH_NODE_LOCATION, nv=5, binary=FALSE, numeric=FALSE
MENOPAUSE_STATUS, nv=4, binary=FALSE, numeric=FALSE
LYMPHOVASCULAR_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
LYMPH_NODES_EXAMINED_HE_COUNT, nv=10, binary=FALSE, numeric=TRUE
LYMPH_NODES_EXAMINED, nv=49, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=20, binary=FALSE, numeric=TRUE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=36, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CHEMO_CONCURRENT_TYPE, nv=3, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=17, binary=FALSE, numeric=TRUE
AGE_AT_DIAGNOSIS, nv=61, binary=FALSE, numeric=TRUE
CLINICAL_STAGE, nv=17, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    63  20
  1P GAIN WILD-TYPE 148  47
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               83               195 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20                47 
$`1P GAIN MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1M7 
       49.48        36.56       177.04        82.85        31.40        46.32 
TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A2LZ TCGA-C5-A3HF 
       38.99         0.46         2.43        20.91       100.14        17.85 
TCGA-C5-A7CJ TCGA-C5-A7X8 TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KL TCGA-DR-A0ZL 
      101.82         2.73        23.51        27.52        44.94        87.75 
TCGA-DS-A0VL TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A439 
       55.63        39.55        37.35        31.36        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2GZ 
       26.01        25.91        27.29        27.22         0.36        12.59 
TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA TCGA-EK-A2RN 
        1.51         0.39         0.59         0.36        40.96         0.53 
TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A40J 
        0.03        15.22        19.79        20.98        26.14        14.01 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LC TCGA-IR-A3LL TCGA-JW-A5VK TCGA-JW-AAVH 
       20.78        14.93       129.37        36.36        20.48        18.15 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W 
      209.59        44.61        20.91         0.30         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MY-A5BE TCGA-PN-A8MA 
       19.56         8.35        11.38        28.08        35.05         2.96 
TCGA-Q1-A5R2 TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EH TCGA-VS-A8EJ 
       16.41        19.59        93.99        12.16        32.42        19.96 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X TCGA-VS-A954 TCGA-VS-A957 
       11.51        59.18        31.27        16.64        56.35        55.50 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       51.32        50.47        28.50        24.30        46.92        45.11 
TCGA-VS-A9UL TCGA-VS-A9V2 TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       14.53        18.25        29.26         1.41         3.91 

$`1P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
       18.74       144.16       173.29         5.46        19.86        67.46 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MN 
       30.21        35.01        57.73        53.16        35.61        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG 
       38.43        33.24        52.01        18.02        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      154.32       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC 
      155.77       131.11        94.95         9.34        13.61        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ 
       45.83         8.35       146.86        99.91        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZM 
       14.73         1.12        95.11        82.06        63.98        58.88 
TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76        69.96        95.67        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD 
       17.52         8.28        40.87        30.90        31.53        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       25.02        36.89        26.40         0.30        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
       14.89        26.79        27.25        24.00        13.48        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 
       26.27         6.64        19.27         0.43         1.45         0.13 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK 
        4.31         0.10         0.43        47.77         0.10         0.49 
TCGA-EK-A3GM TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF 
        0.76        20.35         7.92        14.70         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84        19.04        16.11        31.36        36.26 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48        16.14        28.31        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 
       17.75        25.41        16.57        21.67         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16        66.81        96.95        78.71        81.96        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        28.37 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU 
        8.28        21.11        11.28         0.89        12.49        13.35 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
       17.82        19.56         8.52        34.62        19.96        54.81 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       20.84        17.23        15.58        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       14.60        11.67        69.50        10.03        46.52        45.57 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH 
       23.97        65.49        32.15        53.59        36.13        39.78 
TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       40.87         4.73        33.37        40.14        58.45        15.68 
TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ 
       50.14        43.40        48.39        29.95        27.12         1.71 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ 
       17.75         4.34        16.24        15.42        26.01        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
       19.13         0.69         0.16 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           209.59            210.67 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            24.56             21.67 
[1] "0.0 - 209.6 (24.6)" "0.1 - 210.7 (21.7)"
[1] "hr=" "1"  
D1V2, continuous
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED    35  24  10   1
  1P GAIN WILD-TYPE 100  46  11   7
D1V3, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              35               100
  T2              24                46
  T3              10                11
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   36 17
  1P GAIN WILD-TYPE 93 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     36   17
  1P GAIN WILD-TYPE   93   39
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              36                93
  1              17                39
[1] 2 2
[1] FALSE
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   35  3
  1P GAIN WILD-TYPE 73  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     35    3
  1P GAIN WILD-TYPE   73    7
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              35                73
  1               3                 7
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   16 35
  1P GAIN WILD-TYPE 39 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     16   35
  1P GAIN WILD-TYPE   39   88
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               16                39
  YES              35                88
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED               0                               84
  1P GAIN WILD-TYPE             6                              158
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1P GAIN MUTATED                                               1
  1P GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1P GAIN MUTATED                                     3
  1P GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1P GAIN MUTATED                                           0
  1P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1P GAIN MUTATED                                              2
  1P GAIN WILD-TYPE                                           15
D1V7, multiclass
                                               clus
vv                                              1P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           84
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              1P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            158
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
D1V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  1     9
  1P GAIN WILD-TYPE                                7    10
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED                          12
  1P GAIN WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           0    58
  1P GAIN WILD-TYPE                                         2   144
D1V10, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   9                10
  BLACK OR AFRICAN AMERICAN                              12                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  58               144
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     7  50
  1P GAIN WILD-TYPE  16 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      7   50
  1P GAIN WILD-TYPE   16  112
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                16
  NOT HISPANIC OR LATINO              50               112
[1] 2 2
[1] FALSE
D1V12, continuous
D1V13, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    56  22
  1P GAIN WILD-TYPE 127  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     56   22
  1P GAIN WILD-TYPE  127   52
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  TUMOR FREE              56               127
  WITH TUMOR              22                52
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  1P GAIN MUTATED    4 43 40  0  3
  1P GAIN WILD-TYPE 14 86 75  1 21
D1V14, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  G1               4                14
  G2              43                86
  G3              40                75
  G4               0                 1
  GX               3                21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, continuous
D1V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  1P GAIN MUTATED                                             7
  1P GAIN WILD-TYPE                                          31
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  1P GAIN MUTATED                                        4
  1P GAIN WILD-TYPE                                      5
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  1P GAIN MUTATED                                                 1
  1P GAIN WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1P GAIN MUTATED               20                  44
  1P GAIN WILD-TYPE             42                  99
D1V17, multiclass
                                                 clus
vv                                                1P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               20
  LIFELONG NON-SMOKER                                          44
                                                 clus
vv                                                1P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 42
  LIFELONG NON-SMOKER                                            99
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V18, continuous
D1V19, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    6  1
  1P GAIN WILD-TYPE 19  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6    1
  1P GAIN WILD-TYPE   19    2
                         clus
vv                        1P GAIN MUTATED 1P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  6                19
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D1V20, continuous
D1V21, continuous
D1V22, continuous
D1V23, continuous
D1V24, continuous
D1V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  1P GAIN MUTATED                                     1
  1P GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  1P GAIN MUTATED                                     0                      10
  1P GAIN WILD-TYPE                                   7                      26
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1P GAIN MUTATED                         0                       2
  1P GAIN WILD-TYPE                       1                       6
D1V26, multiclass
                                     clus
vv                                    1P GAIN MUTATED 1P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                          10                26
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  1P GAIN MUTATED                                               0
  1P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  1P GAIN MUTATED                                                7
  1P GAIN WILD-TYPE                                             18
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1P GAIN MUTATED                                                                                  37
  1P GAIN WILD-TYPE                                                                                45
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1P GAIN MUTATED                                                                                             30
  1P GAIN WILD-TYPE                                                                                           91
D1V27, multiclass
                                                                                              clus
vv                                                                                             1P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         37
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              30
                                                                                              clus
vv                                                                                             1P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V28, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   20 23
  1P GAIN WILD-TYPE 51 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     20   23
  1P GAIN WILD-TYPE   51   51
         clus
vv        1P GAIN MUTATED 1P GAIN WILD-TYPE
  ABSENT               20                51
  PRESENT              23                51
[1] 2 2
[1] FALSE
D1V29, continuous
D1V30, continuous
D1V31, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   16 38
  1P GAIN WILD-TYPE 33 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     16   38
  1P GAIN WILD-TYPE   33   79
                                          clus
vv                                         1P GAIN MUTATED 1P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  16                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              38                79
[1] 2 2
[1] FALSE
D1V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1P GAIN MUTATED              3          10         28
  1P GAIN WILD-TYPE           12          44         57
D1V33, multiclass
              clus
vv             1P GAIN MUTATED 1P GAIN WILD-TYPE
  CURRENT USER               3                12
  FORMER USER               10                44
  NEVER USED                28                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V34, continuous
D1V35, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   26  7
  1P GAIN WILD-TYPE 66 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     26    7
  1P GAIN WILD-TYPE   66   11
         clus
vv        1P GAIN MUTATED 1P GAIN WILD-TYPE
  ABSENT               26                66
  PRESENT               7                11
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  1P GAIN MUTATED             1        26     0
  1P GAIN WILD-TYPE           4        74     2
D1V36, multiclass
             clus
vv            1P GAIN MUTATED 1P GAIN WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                26                74
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V37, continuous
D1V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  1P GAIN MUTATED         0        0         0         0       11        25
  1P GAIN WILD-TYPE       5        1         1         1       23        52
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  1P GAIN MUTATED           6        1         2          3          2
  1P GAIN WILD-TYPE        31        3         6          2          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  1P GAIN MUTATED          13         1          2         19         2
  1P GAIN WILD-TYPE        31         0          1         23         5
                   vv
clus                STAGE IVB
  1P GAIN MUTATED           1
  1P GAIN WILD-TYPE        11
D1V39, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                11                23
  STAGE IB1               25                52
  STAGE IB2                6                31
  STAGE II                 1                 3
  STAGE IIA                2                 6
  STAGE IIA1               3                 2
  STAGE IIA2               2                 5
  STAGE IIB               13                31
  STAGE III                1                 0
  STAGE IIIA               2                 1
  STAGE IIIB              19                23
  STAGE IVA                2                 5
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    99  33
  1Q GAIN WILD-TYPE 112  34
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              132               146 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               33                34 
$`1Q GAIN MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       49.48        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH 
       82.85         5.46        31.40        46.32        53.16        38.99 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY 
        0.46         2.43        20.91         3.58        44.22        78.35 
TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UI 
      100.14        17.85       101.82       134.33        15.48        94.95 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR 
        2.73        50.99        45.83         8.35        23.51        27.52 
TCGA-DG-A2KH TCGA-DG-A2KL TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A3LQ 
        1.12        44.94        87.75        58.88        55.63        22.98 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT 
       17.52         8.28        39.55        37.35        30.90        31.36 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.56        31.73        26.01        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       27.22        24.00        13.48         0.36        12.59        60.72 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA 
        1.51        19.27         0.39         0.59         0.36        40.96 
TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A449 
        0.53         0.49         0.76         0.03        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI 
       19.79         8.32        15.55        23.84        16.11        20.98 
TCGA-FU-A40J TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LC 
       14.01        16.57        20.78        14.93         9.44       129.37 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 
       36.36        21.44        20.48         8.28        18.15       209.59 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W 
       44.61        20.91        11.28         0.30         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MY-A5BE 
       19.56         8.35         8.52        11.38        28.08        35.05 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V 
        2.96        16.41        15.95         9.34        18.64        19.59 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL 
       93.99        12.16        10.03        32.42        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94X 
       32.15        53.59        11.51        59.18        31.27        16.64 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA 
       56.35        55.50        51.32        50.47        43.40        28.50 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP 
       24.30        46.92        45.11        14.53        27.25        47.47 
TCGA-VS-A9UV TCGA-VS-A9V2 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
        3.42        18.25        26.01        29.26         1.41         3.91 

$`1Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        57.04        23.67        11.44        68.84 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI 
       19.86        67.46        30.21        35.01        57.73        35.61 
TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 
       40.93        73.18        73.45        83.05        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM 
       52.01        18.02        20.42       210.67       154.32        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        17.19       155.77       131.11         9.34        13.61 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ 
      146.86        99.91        20.81        20.91        14.73        95.11 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       82.06        63.98        36.76        69.96        95.67        16.83 
TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       16.18        40.87        31.53        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.40         0.30        24.82         7.46        14.89        26.79 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC 
       26.27         6.64         0.43         1.45         0.13         4.31 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.43        47.77         0.10        20.35         7.92 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        1.22        19.04        31.36        36.26        26.14         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       16.14        28.31        35.44        10.55         1.12        17.75 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF 
       25.41        21.67       147.39       137.16        66.81        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        29.85        27.42         3.29        24.56 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU 
       15.58        28.37        21.11         0.89        12.49        13.35 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF 
       17.82        19.56        34.62        19.96        54.81        20.84 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       17.23        15.58         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EC 
       15.88        22.62        14.60        11.67        69.50        46.52 
TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A94W TCGA-VS-A94Y 
       45.57        23.97        36.13        39.78        40.87         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A958 TCGA-VS-A9U7 
       33.37        40.14        58.45        15.68        50.14        48.39 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR 
       29.95        27.12         1.71        47.87        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       15.85        14.53        18.25        67.20        18.84         5.16 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       17.75         4.34        16.24        15.42        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
        0.69         0.16 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           209.59            210.67 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            22.75             23.82 
[1] "0.0 - 209.6 (22.8)" "0.1 - 210.7 (23.8)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED   55 37 13  3
  1Q GAIN WILD-TYPE 80 33  8  5
D2V3, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              55                80
  T2              37                33
  T3              13                 8
  T4               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   59 24
  1Q GAIN WILD-TYPE 70 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     59   24
  1Q GAIN WILD-TYPE   70   32
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              59                70
  1              24                32
[1] 2 2
[1] FALSE
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   52  7
  1Q GAIN WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     52    7
  1Q GAIN WILD-TYPE   56    3
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              52                56
  1               7                 3
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   27 57
  1Q GAIN WILD-TYPE 28 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     27   57
  1Q GAIN WILD-TYPE   28   66
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               27                28
  YES              57                66
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED               3                              122
  1Q GAIN WILD-TYPE             3                              120
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1Q GAIN MUTATED                                               3
  1Q GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1Q GAIN MUTATED                                     8
  1Q GAIN WILD-TYPE                                  13
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1Q GAIN MUTATED                                           0
  1Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1Q GAIN MUTATED                                              4
  1Q GAIN WILD-TYPE                                           13
D2V7, multiclass
                                               clus
vv                                              1Q GAIN MUTATED
  ADENOSQUAMOUS                                               3
  CERVICAL SQUAMOUS CELL CARCINOMA                          122
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                4
                                               clus
vv                                              1Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 3
  CERVICAL SQUAMOUS CELL CARCINOMA                            120
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
D2V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1    13
  1Q GAIN WILD-TYPE                                7     6
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED                          18
  1Q GAIN WILD-TYPE                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           0    94
  1Q GAIN WILD-TYPE                                         2   108
D2V10, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                  13                 6
  BLACK OR AFRICAN AMERICAN                              18                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  94               108
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   10 76
  1Q GAIN WILD-TYPE 13 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     10   76
  1Q GAIN WILD-TYPE   13   86
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  10                13
  NOT HISPANIC OR LATINO              76                86
[1] 2 2
[1] FALSE
D2V12, continuous
D2V13, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   88 36
  1Q GAIN WILD-TYPE 95 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     88   36
  1Q GAIN WILD-TYPE   95   38
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  TUMOR FREE              88                95
  WITH TUMOR              36                38
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  1Q GAIN MUTATED    6 62 61  0  9
  1Q GAIN WILD-TYPE 12 67 54  1 15
D2V14, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  G1               6                12
  G2              62                67
  G3              61                54
  G4               0                 1
  GX               9                15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, continuous
D2V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  1Q GAIN MUTATED                                            14
  1Q GAIN WILD-TYPE                                          24
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  1Q GAIN MUTATED                                        5
  1Q GAIN WILD-TYPE                                      4
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  1Q GAIN MUTATED                                                 2
  1Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1Q GAIN MUTATED               33                  69
  1Q GAIN WILD-TYPE             29                  74
D2V17, multiclass
                                                 clus
vv                                                1Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               2
  CURRENT SMOKER                                               33
  LIFELONG NON-SMOKER                                          69
                                                 clus
vv                                                1Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 29
  LIFELONG NON-SMOKER                                            74
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V18, continuous
D2V19, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   14  2
  1Q GAIN WILD-TYPE 11  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     14    2
  1Q GAIN WILD-TYPE   11    1
                         clus
vv                        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                 14                11
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
D2V20, continuous
D2V21, continuous
D2V22, continuous
D2V23, continuous
D2V24, continuous
D2V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  1Q GAIN MUTATED                                     1
  1Q GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  1Q GAIN MUTATED                                     1                      19
  1Q GAIN WILD-TYPE                                   6                      17
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1Q GAIN MUTATED                         0                       3
  1Q GAIN WILD-TYPE                       1                       5
D2V26, multiclass
                                     clus
vv                                    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 6
  OTHER LOCATION, SPECIFY                          19                17
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           3                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  1Q GAIN MUTATED                                               0
  1Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  1Q GAIN MUTATED                                               12
  1Q GAIN WILD-TYPE                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1Q GAIN MUTATED                                                                                  47
  1Q GAIN WILD-TYPE                                                                                35
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1Q GAIN MUTATED                                                                                             54
  1Q GAIN WILD-TYPE                                                                                           67
D2V27, multiclass
                                                                                              clus
vv                                                                                             1Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         47
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              54
                                                                                              clus
vv                                                                                             1Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           35
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V28, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   29 36
  1Q GAIN WILD-TYPE 42 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     29   36
  1Q GAIN WILD-TYPE   42   38
         clus
vv        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ABSENT               29                42
  PRESENT              36                38
[1] 2 2
[1] FALSE
D2V29, continuous
D2V30, continuous
D2V31, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   21 59
  1Q GAIN WILD-TYPE 28 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     21   59
  1Q GAIN WILD-TYPE   28   58
                                          clus
vv                                         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  21                28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              59                58
[1] 2 2
[1] FALSE
D2V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1Q GAIN MUTATED              4          23         39
  1Q GAIN WILD-TYPE           11          31         46
D2V33, multiclass
              clus
vv             1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CURRENT USER               4                11
  FORMER USER               23                31
  NEVER USED                39                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V34, continuous
D2V35, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   38  8
  1Q GAIN WILD-TYPE 54 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     38    8
  1Q GAIN WILD-TYPE   54   10
         clus
vv        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ABSENT               38                54
  PRESENT               8                10
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  1Q GAIN MUTATED             1        48     0
  1Q GAIN WILD-TYPE           4        52     2
D2V36, multiclass
             clus
vv            1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                48                52
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V37, continuous
D2V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  1Q GAIN MUTATED         2        0         0         0       14        36
  1Q GAIN WILD-TYPE       3        1         1         1       20        41
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  1Q GAIN MUTATED          14        2         4          4          3
  1Q GAIN WILD-TYPE        23        2         4          1          4
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  1Q GAIN MUTATED          20         1          2         25         4
  1Q GAIN WILD-TYPE        24         0          1         17         3
                   vv
clus                STAGE IVB
  1Q GAIN MUTATED           5
  1Q GAIN WILD-TYPE         7
D2V39, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                14                20
  STAGE IB1               36                41
  STAGE IB2               14                23
  STAGE II                 2                 2
  STAGE IIA                4                 4
  STAGE IIA1               4                 1
  STAGE IIA2               3                 4
  STAGE IIB               20                24
  STAGE III                1                 0
  STAGE IIIA               2                 1
  STAGE IIIB              25                17
  STAGE IVA                4                 3
  STAGE IVB                5                 7
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    45  15
  2P GAIN WILD-TYPE 166  52
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               60               218 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               15                52 
$`2P GAIN MUTATED`
TCGA-BI-A20A TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ 
       23.67         5.46        31.40        57.73        35.61         0.46 
TCGA-C5-A2LT TCGA-C5-A2M2 TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       73.18        33.24       131.11         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A3LQ 
       50.99        23.51         1.12        95.11        44.94        22.98 
TCGA-DS-A7WH TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A5ZF 
       17.52        24.56        31.73        26.01        14.89        27.22 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2RA TCGA-EK-A3GJ 
       12.59        26.27        19.27         0.59        40.96         0.10 
TCGA-EX-A1H6 TCGA-FU-A23L TCGA-FU-A40J TCGA-IR-A3LC TCGA-JW-A5VJ TCGA-JX-A5QV 
        7.92        23.84        14.01       129.37        21.44        20.91 
TCGA-MA-AA41 TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73S TCGA-UC-A7PD 
        8.35        17.23        16.41        15.95        22.62        11.67 
TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 
       93.99        23.97        59.18        16.64         4.73        58.45 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       51.32        50.47        43.40        29.95        27.12        24.30 
TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-WL-A834 
       45.11        14.53        47.47        17.75        16.24        26.01 

$`2P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF 
       19.86        67.46        46.32        30.21        35.01        53.16 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD 
       73.45        83.05        78.35       100.14        38.43        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19       155.77 
TCGA-C5-A7UI TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR 
       94.95        45.83         8.35       146.86        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.81        20.91        14.73        82.06        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        36.76        55.63        69.96        95.67        16.83 
TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18         8.28        39.55        40.87        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
        0.30        24.82         7.46        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP 
       27.25        24.00        13.48         0.36        60.72         6.64 
TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51         0.39         0.43         0.36         1.45         0.13 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK 
        4.31         0.10         0.43        47.77         0.53         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.76         0.03        20.35        15.22        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        8.32        15.55         1.22        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26        20.98        26.14         1.48        16.14        28.31 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       35.44        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
       66.81        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
        8.28        18.15        21.11       209.59        44.61        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
        0.89        12.49         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       19.56        17.82        19.56         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI 
        9.34        18.64        19.59        14.60        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        46.52        45.57        32.42        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        53.59        36.13        11.51        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       40.87        33.37        40.14        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UM 
       50.14        48.39        28.50        46.92         1.71        27.25 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.87        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V4 
       18.25        67.20        18.84         5.16        18.25         4.34 
TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       15.42        29.26        67.59        19.13         0.69         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           131.11            210.67 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           23.755            21.390 
[1] "0.1 - 131.1 (23.8)" "0.0 - 210.7 (21.4)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED    24  17   5   2
  2P GAIN WILD-TYPE 111  53  16   6
D3V3, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              24               111
  T2              17                53
  T3               5                16
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    24  10
  2P GAIN WILD-TYPE 105  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     24   10
  2P GAIN WILD-TYPE  105   46
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              24               105
  1              10                46
[1] 2 2
[1] FALSE
D3V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   22  3
  2P GAIN WILD-TYPE 86  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     22    3
  2P GAIN WILD-TYPE   86    7
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              22                86
  1               3                 7
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    9 32
  2P GAIN WILD-TYPE 46 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      9   32
  2P GAIN WILD-TYPE   46   91
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                9                46
  YES              32                91
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED               2                               50
  2P GAIN WILD-TYPE             4                              192
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2P GAIN MUTATED                                               1
  2P GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2P GAIN MUTATED                                     5
  2P GAIN WILD-TYPE                                  16
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2P GAIN MUTATED                                           1
  2P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2P GAIN MUTATED                                              5
  2P GAIN WILD-TYPE                                           12
D3V7, multiclass
                                               clus
vv                                              2P GAIN MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                           50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                5
                                               clus
vv                                              2P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            192
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  2     2
  2P GAIN WILD-TYPE                                6    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED                           4
  2P GAIN WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           1    44
  2P GAIN WILD-TYPE                                         1   158
D3V10, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 6
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               4                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 1
  WHITE                                                  44               158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     4  28
  2P GAIN WILD-TYPE  19 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4   28
  2P GAIN WILD-TYPE   19  134
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                19
  NOT HISPANIC OR LATINO              28               134
[1] 2 2
[1] FALSE
D3V12, continuous
D3V13, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    35  22
  2P GAIN WILD-TYPE 148  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     35   22
  2P GAIN WILD-TYPE  148   52
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  TUMOR FREE              35               148
  WITH TUMOR              22                52
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  2P GAIN MUTATED     3  24  31   0   5
  2P GAIN WILD-TYPE  15 105  84   1  19
D3V14, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  G1               3                15
  G2              24               105
  G3              31                84
  G4               0                 1
  GX               5                19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, continuous
D3V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2P GAIN MUTATED                                             7
  2P GAIN WILD-TYPE                                          31
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  2P GAIN MUTATED                                        1
  2P GAIN WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  2P GAIN MUTATED                                                 1
  2P GAIN WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2P GAIN MUTATED               13                  31
  2P GAIN WILD-TYPE             49                 112
D3V17, multiclass
                                                 clus
vv                                                2P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               13
  LIFELONG NON-SMOKER                                          31
                                                 clus
vv                                                2P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 49
  LIFELONG NON-SMOKER                                           112
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V18, continuous
D3V19, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    5  0
  2P GAIN WILD-TYPE 20  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5    0
  2P GAIN WILD-TYPE   20    3
                         clus
vv                        2P GAIN MUTATED 2P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D3V20, continuous
D3V21, continuous
D3V22, continuous
D3V23, continuous
D3V24, continuous
D3V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  2P GAIN MUTATED                                     0
  2P GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  2P GAIN MUTATED                                     2                       7
  2P GAIN WILD-TYPE                                   5                      29
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2P GAIN MUTATED                         0                       1
  2P GAIN WILD-TYPE                       1                       7
D3V26, multiclass
                                     clus
vv                                    2P GAIN MUTATED 2P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 5
  OTHER LOCATION, SPECIFY                           7                29
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  2P GAIN MUTATED                                               0
  2P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  2P GAIN MUTATED                                                5
  2P GAIN WILD-TYPE                                             20
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2P GAIN MUTATED                                                                                  18
  2P GAIN WILD-TYPE                                                                                64
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2P GAIN MUTATED                                                                                             25
  2P GAIN WILD-TYPE                                                                                           96
D3V27, multiclass
                                                                                              clus
vv                                                                                             2P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              25
                                                                                              clus
vv                                                                                             2P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V28, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   12 16
  2P GAIN WILD-TYPE 59 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     12   16
  2P GAIN WILD-TYPE   59   58
         clus
vv        2P GAIN MUTATED 2P GAIN WILD-TYPE
  ABSENT               12                59
  PRESENT              16                58
[1] 2 2
[1] FALSE
D3V29, continuous
D3V30, continuous
D3V31, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    9 20
  2P GAIN WILD-TYPE 40 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      9   20
  2P GAIN WILD-TYPE   40   97
                                          clus
vv                                         2P GAIN MUTATED 2P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   9                40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              20                97
[1] 2 2
[1] FALSE
D3V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2P GAIN MUTATED              4          15         18
  2P GAIN WILD-TYPE           11          39         67
D3V33, multiclass
              clus
vv             2P GAIN MUTATED 2P GAIN WILD-TYPE
  CURRENT USER               4                11
  FORMER USER               15                39
  NEVER USED                18                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V34, continuous
D3V35, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   15  6
  2P GAIN WILD-TYPE 77 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15    6
  2P GAIN WILD-TYPE   77   12
         clus
vv        2P GAIN MUTATED 2P GAIN WILD-TYPE
  ABSENT               15                77
  PRESENT               6                12
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  2P GAIN MUTATED             2        25     1
  2P GAIN WILD-TYPE           3        75     1
D3V36, multiclass
             clus
vv            2P GAIN MUTATED 2P GAIN WILD-TYPE
  CARBOPLATIN               2                 3
  CISPLATIN                25                75
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V37, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                15 
       TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A1MP 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-ZX-AA5X 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
D3V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  2P GAIN MUTATED         0        0         0         0        3        20
  2P GAIN WILD-TYPE       5        1         1         1       31        57
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  2P GAIN MUTATED           5        0         3          2          1
  2P GAIN WILD-TYPE        32        4         5          3          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  2P GAIN MUTATED          14         0          1          9         0
  2P GAIN WILD-TYPE        30         1          2         33         7
                   vv
clus                STAGE IVB
  2P GAIN MUTATED           3
  2P GAIN WILD-TYPE         9
D3V39, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 3                31
  STAGE IB1               20                57
  STAGE IB2                5                32
  STAGE II                 0                 4
  STAGE IIA                3                 5
  STAGE IIA1               2                 3
  STAGE IIA2               1                 6
  STAGE IIB               14                30
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               9                33
  STAGE IVA                0                 7
  STAGE IVB                3                 9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    25   9
  2Q GAIN WILD-TYPE 186  58
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               34               244 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9                58 
$`2Q GAIN MUTATED`
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A2LT TCGA-C5-A7UH 
       23.67        31.40        35.61         0.46        73.18       131.11 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A7WH 
        9.34         2.73        23.51         1.12        95.11        17.52 
TCGA-DS-A7WI TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2H1 
        8.28        31.73        26.01        27.22        12.59        26.27 
TCGA-EK-A2PI TCGA-EK-A2PM TCGA-FU-A40J TCGA-MA-AA41 TCGA-MY-A913 TCGA-Q1-A73S 
       19.27         0.59        14.01         8.35        17.23        22.62 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A959 TCGA-VS-A9UB 
       11.67        93.99        23.97        59.18        51.32        29.95 
TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9V3 TCGA-WL-A834 
       24.30        14.53        17.75        26.01 

$`2Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
        5.46        19.86        67.46        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       57.73        53.16        38.99         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
        3.58        44.22        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      210.67       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC 
      147.35        17.19       155.77        94.95        13.61        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83         8.35       146.86        99.91        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.91        14.73        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76        55.63        69.96        95.67        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.83        16.18        39.55        40.87        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       24.56         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       25.91        27.29        27.25        24.00        13.48         0.36 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 
       60.72         6.64         1.51         0.39         0.43         0.36 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK 
        1.45         0.13        40.96         4.31         0.10         0.43 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN 
       47.77         0.53         0.10         0.49         0.76         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92        15.22        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       15.55         1.22        23.84        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26        20.98        26.14         1.48        16.14        28.31 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       35.44        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       129.37        96.95        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        28.37         8.28        18.15        21.11       209.59 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
       44.61        20.91        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.82        13.35        22.52        19.56        17.82        19.56 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       35.05        20.84         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
       18.64        19.59        14.60        12.16        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       46.52        45.57        32.42        19.96        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       53.59        36.13        11.51        39.78        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       16.64         4.73        33.37        40.14        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       56.35        55.50        50.14        50.47        43.40        48.39 
TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM 
       28.50        27.12        46.92        45.11         1.71        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       47.87        47.47        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
        4.34        16.24        15.42        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.46              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           131.11            210.67 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            23.59             22.75 
[1] "0.5 - 131.1 (23.6)" "0.0 - 210.7 (22.8)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED    14   7   4   1
  2Q GAIN WILD-TYPE 121  63  17   7
D4V3, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              14               121
  T2               7                63
  T3               4                17
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    11  10
  2Q GAIN WILD-TYPE 118  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     11   10
  2Q GAIN WILD-TYPE  118   46
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              11               118
  1              10                46
[1] 2 2
[1] FALSE
D4V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   13  2
  2Q GAIN WILD-TYPE 95  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     13    2
  2Q GAIN WILD-TYPE   95    8
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              13                95
  1               2                 8
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     3  20
  2Q GAIN WILD-TYPE  52 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   20
  2Q GAIN WILD-TYPE   52  103
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                3                52
  YES              20               103
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED               2                               31
  2Q GAIN WILD-TYPE             4                              211
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2Q GAIN MUTATED                                               0
  2Q GAIN WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2Q GAIN MUTATED                                     2
  2Q GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2Q GAIN MUTATED                                           0
  2Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2Q GAIN MUTATED                                              2
  2Q GAIN WILD-TYPE                                           15
D4V7, multiclass
                                               clus
vv                                              2Q GAIN MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                           31
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              2Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            211
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
D4V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  1     2
  2Q GAIN WILD-TYPE                                7    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED                           2
  2Q GAIN WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           0    26
  2Q GAIN WILD-TYPE                                         2   176
D4V10, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               2                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  26               176
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  18
  2Q GAIN WILD-TYPE  21 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   18
  2Q GAIN WILD-TYPE   21  144
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                21
  NOT HISPANIC OR LATINO              18               144
[1] 2 2
[1] FALSE
D4V12, continuous
D4V13, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    20  13
  2Q GAIN WILD-TYPE 163  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     20   13
  2Q GAIN WILD-TYPE  163   61
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  TUMOR FREE              20               163
  WITH TUMOR              13                61
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  2Q GAIN MUTATED     0  17  17   0   2
  2Q GAIN WILD-TYPE  18 112  98   1  22
D4V14, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  G1               0                18
  G2              17               112
  G3              17                98
  G4               0                 1
  GX               2                22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, continuous
D4V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2Q GAIN MUTATED                                             4
  2Q GAIN WILD-TYPE                                          34
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  2Q GAIN MUTATED                                        0
  2Q GAIN WILD-TYPE                                      9
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  2Q GAIN MUTATED                                                 1
  2Q GAIN WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2Q GAIN MUTATED                7                  16
  2Q GAIN WILD-TYPE             55                 127
D4V17, multiclass
                                                 clus
vv                                                2Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                7
  LIFELONG NON-SMOKER                                          16
                                                 clus
vv                                                2Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    34
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 55
  LIFELONG NON-SMOKER                                           127
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V18, continuous
D4V19, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3  0
  2Q GAIN WILD-TYPE 22  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    0
  2Q GAIN WILD-TYPE   22    3
                         clus
vv                        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  3                22
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D4V20, continuous
D4V21, continuous
D4V22, continuous
D4V23, continuous
D4V24, continuous
D4V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  2Q GAIN MUTATED                                     0
  2Q GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  2Q GAIN MUTATED                                     2                       4
  2Q GAIN WILD-TYPE                                   5                      32
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2Q GAIN MUTATED                         0                       0
  2Q GAIN WILD-TYPE                       1                       8
D4V26, multiclass
                                     clus
vv                                    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 5
  OTHER LOCATION, SPECIFY                           4                32
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  2Q GAIN MUTATED                                               0
  2Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  2Q GAIN MUTATED                                                2
  2Q GAIN WILD-TYPE                                             23
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2Q GAIN MUTATED                                                                                   9
  2Q GAIN WILD-TYPE                                                                                73
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2Q GAIN MUTATED                                                                                             16
  2Q GAIN WILD-TYPE                                                                                          105
D4V27, multiclass
                                                                                              clus
vv                                                                                             2Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              16
                                                                                              clus
vv                                                                                             2Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           73
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V28, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4 13
  2Q GAIN WILD-TYPE 67 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   13
  2Q GAIN WILD-TYPE   67   61
         clus
vv        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ABSENT                4                67
  PRESENT              13                61
[1] 2 2
[1] FALSE
D4V29, continuous
D4V30, continuous
D4V31, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     5  14
  2Q GAIN WILD-TYPE  44 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5   14
  2Q GAIN WILD-TYPE   44  103
                                          clus
vv                                         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              14               103
[1] 2 2
[1] FALSE
D4V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2Q GAIN MUTATED              1           9          8
  2Q GAIN WILD-TYPE           14          45         77
D4V33, multiclass
              clus
vv             2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CURRENT USER               1                14
  FORMER USER                9                45
  NEVER USED                 8                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V34, continuous
D4V35, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    7  4
  2Q GAIN WILD-TYPE 85 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      7    4
  2Q GAIN WILD-TYPE   85   14
         clus
vv        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ABSENT                7                85
  PRESENT               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  2Q GAIN MUTATED             0        16     1
  2Q GAIN WILD-TYPE           5        84     1
D4V36, multiclass
             clus
vv            2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                16                84
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V37, continuous
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-MA-AA42        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-ZX-AA5X 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
D4V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  2Q GAIN MUTATED         0        0         0         0        3        11
  2Q GAIN WILD-TYPE       5        1         1         1       31        66
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  2Q GAIN MUTATED           2        0         1          1          1
  2Q GAIN WILD-TYPE        35        4         7          4          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  2Q GAIN MUTATED           7         0          1          8         0
  2Q GAIN WILD-TYPE        37         1          2         34         7
                   vv
clus                STAGE IVB
  2Q GAIN MUTATED           1
  2Q GAIN WILD-TYPE        11
D4V39, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 3                31
  STAGE IB1               11                66
  STAGE IB2                2                35
  STAGE II                 0                 4
  STAGE IIA                1                 7
  STAGE IIA1               1                 4
  STAGE IIA2               1                 6
  STAGE IIB                7                37
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               8                34
  STAGE IVA                0                 7
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    45  23
  3P GAIN WILD-TYPE 166  44
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               68               210 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               23                44 
$`3P GAIN MUTATED`
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ 
       46.32        30.21        35.01        53.16        38.99         0.46 
TCGA-C5-A1ML TCGA-C5-A2LT TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CJ 
       20.91        73.18        33.24        18.02        17.85       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-DG-A2KH 
      134.33        15.48         9.34        50.99         8.35         1.12 
TCGA-DG-A2KJ TCGA-DS-A0VL TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A439 
       95.11        55.63        17.52         8.28        39.55        31.73 
TCGA-EA-A50E TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM 
        7.46        27.22        12.59         1.51        19.27         0.59 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A3GM TCGA-EX-A69L TCGA-FU-A3TX TCGA-GH-A9DA 
        0.13        40.96         0.76        19.79         1.48        17.75 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LA TCGA-JW-A852 TCGA-JX-A3Q0 
       25.41        21.67        20.78       137.16         8.28       209.59 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A7HU TCGA-MA-AA41 TCGA-MU-A8JM TCGA-PN-A8MA 
       44.61        11.28        13.35         8.35        19.96         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A73O TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EI 
       15.58        14.07        11.67        12.16        10.03        23.97 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       19.96        65.49        36.13        59.18        31.27        40.87 
TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UV 
       55.50        51.32        24.30        46.92        45.11         3.42 
TCGA-VS-AA62 TCGA-ZJ-AAXA 
       15.42         1.41 

$`3P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1ME 
       82.85         5.46        19.86        67.46        31.40        57.73 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
       35.61         2.43        40.93         3.58        44.22        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HL 
       83.05        78.35       100.14        38.43        52.01        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      210.67       154.32        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XJ 
      131.11        94.95        13.61         2.73        45.83       146.86 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52        20.81        20.91        14.73 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A1QT 
       69.96        95.67        22.98        16.83        16.18        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       36.89        26.40        24.56        26.01         0.30        24.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       14.89        26.79        25.91        27.29        27.25        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PK 
       13.48         0.36        60.72        26.27         6.64         0.39 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK 
        0.43         0.36         1.45         4.31         0.10         0.43 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
       47.77         0.53         0.10         0.49         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        7.92        15.22        14.70         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
       26.14        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-HG-A9SC TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
        1.12        16.57        14.93         9.44       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX 
       28.37        18.15        21.11        20.91         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.30         0.82        22.52        19.56        17.82        19.56 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE 
        8.52        11.38        28.08        34.62        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       20.84        17.23        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       17.56        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       14.60        93.99        69.50        46.52        45.57        32.42 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y 
       32.15        53.59        11.51        39.78        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 
       33.37        40.14        58.45        15.68        56.35        50.14 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       50.47        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
        1.71        14.53        27.25        47.87        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       26.07        15.85        14.53        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-WL-A834 
        5.16        18.25        17.75         4.34        16.24        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26        67.59        19.13         0.69         0.16         3.91 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.13              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           209.59            210.67 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            20.37             23.92 
[1] "0.1 - 209.6 (20.4)" "0.0 - 210.7 (23.9)"
[1] "hr=" "1.7"
D5V2, continuous
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED    28  17   7   3
  3P GAIN WILD-TYPE 107  53  14   5
D5V3, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              28               107
  T2              17                53
  T3               7                14
  T4               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   30 13
  3P GAIN WILD-TYPE 99 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     30   13
  3P GAIN WILD-TYPE   99   43
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              30                99
  1              13                43
[1] 2 2
[1] FALSE
D5V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   23  4
  3P GAIN WILD-TYPE 85  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     23    4
  3P GAIN WILD-TYPE   85    6
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              23                85
  1               4                 6
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   13 32
  3P GAIN WILD-TYPE 42 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     13   32
  3P GAIN WILD-TYPE   42   91
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               13                42
  YES              32                91
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED               1                               60
  3P GAIN WILD-TYPE             5                              182
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3P GAIN MUTATED                                               0
  3P GAIN WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3P GAIN MUTATED                                     6
  3P GAIN WILD-TYPE                                  15
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3P GAIN MUTATED                                           1
  3P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3P GAIN MUTATED                                              3
  3P GAIN WILD-TYPE                                           14
D5V7, multiclass
                                               clus
vv                                              3P GAIN MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           60
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                3
                                               clus
vv                                              3P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            182
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  1     7
  3P GAIN WILD-TYPE                                7    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED                           8
  3P GAIN WILD-TYPE                        20
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           0    44
  3P GAIN WILD-TYPE                                         2   158
D5V10, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   7                12
  BLACK OR AFRICAN AMERICAN                               8                20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  44               158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     5  34
  3P GAIN WILD-TYPE  18 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5   34
  3P GAIN WILD-TYPE   18  128
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                18
  NOT HISPANIC OR LATINO              34               128
[1] 2 2
[1] FALSE
D5V12, continuous
D5V13, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    36  26
  3P GAIN WILD-TYPE 147  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     36   26
  3P GAIN WILD-TYPE  147   48
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  TUMOR FREE              36               147
  WITH TUMOR              26                48
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  3P GAIN MUTATED    1 32 27  0  9
  3P GAIN WILD-TYPE 17 97 88  1 15
D5V14, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  G1               1                17
  G2              32                97
  G3              27                88
  G4               0                 1
  GX               9                15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, continuous
D5V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3P GAIN MUTATED                                             9
  3P GAIN WILD-TYPE                                          29
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  3P GAIN MUTATED                                        2
  3P GAIN WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  3P GAIN MUTATED                                                 1
  3P GAIN WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3P GAIN MUTATED               15                  33
  3P GAIN WILD-TYPE             47                 110
D5V17, multiclass
                                                 clus
vv                                                3P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               15
  LIFELONG NON-SMOKER                                          33
                                                 clus
vv                                                3P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 47
  LIFELONG NON-SMOKER                                           110
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V18, continuous
D5V19, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    8  0
  3P GAIN WILD-TYPE 17  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      8    0
  3P GAIN WILD-TYPE   17    3
                         clus
vv                        3P GAIN MUTATED 3P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  8                17
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D5V20, continuous
D5V21, continuous
D5V22, continuous
D5V23, continuous
D5V24, continuous
D5V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  3P GAIN MUTATED                                     0
  3P GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  3P GAIN MUTATED                                     1                      12
  3P GAIN WILD-TYPE                                   6                      24
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3P GAIN MUTATED                         1                       1
  3P GAIN WILD-TYPE                       0                       7
D5V26, multiclass
                                     clus
vv                                    3P GAIN MUTATED 3P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 6
  OTHER LOCATION, SPECIFY                          12                24
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  3P GAIN MUTATED                                               1
  3P GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  3P GAIN MUTATED                                                3
  3P GAIN WILD-TYPE                                             22
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3P GAIN MUTATED                                                                                  21
  3P GAIN WILD-TYPE                                                                                61
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3P GAIN MUTATED                                                                                             28
  3P GAIN WILD-TYPE                                                                                           93
D5V27, multiclass
                                                                                              clus
vv                                                                                             3P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              28
                                                                                              clus
vv                                                                                             3P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           61
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V28, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   15 14
  3P GAIN WILD-TYPE 56 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     15   14
  3P GAIN WILD-TYPE   56   60
         clus
vv        3P GAIN MUTATED 3P GAIN WILD-TYPE
  ABSENT               15                56
  PRESENT              14                60
[1] 2 2
[1] FALSE
D5V29, continuous
D5V30, continuous
D5V31, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   12 27
  3P GAIN WILD-TYPE 37 90
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     12   27
  3P GAIN WILD-TYPE   37   90
                                          clus
vv                                         3P GAIN MUTATED 3P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  12                37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              27                90
[1] 2 2
[1] FALSE
D5V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3P GAIN MUTATED              3          12         20
  3P GAIN WILD-TYPE           12          42         65
D5V33, multiclass
              clus
vv             3P GAIN MUTATED 3P GAIN WILD-TYPE
  CURRENT USER               3                12
  FORMER USER               12                42
  NEVER USED                20                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V34, continuous
D5V35, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   19  4
  3P GAIN WILD-TYPE 73 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     19    4
  3P GAIN WILD-TYPE   73   14
         clus
vv        3P GAIN MUTATED 3P GAIN WILD-TYPE
  ABSENT               19                73
  PRESENT               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  3P GAIN MUTATED             0        29     0
  3P GAIN WILD-TYPE           5        71     2
D5V36, multiclass
             clus
vv            3P GAIN MUTATED 3P GAIN WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                29                71
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V37, continuous
D5V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  3P GAIN MUTATED         0        0         0         0        5        19
  3P GAIN WILD-TYPE       5        1         1         1       29        58
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  3P GAIN MUTATED           9        1         2          1          3
  3P GAIN WILD-TYPE        28        3         6          4          4
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  3P GAIN MUTATED          13         1          1         10         4
  3P GAIN WILD-TYPE        31         0          2         32         3
                   vv
clus                STAGE IVB
  3P GAIN MUTATED           1
  3P GAIN WILD-TYPE        11
D5V39, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 5                29
  STAGE IB1               19                58
  STAGE IB2                9                28
  STAGE II                 1                 3
  STAGE IIA                2                 6
  STAGE IIA1               1                 4
  STAGE IIA2               3                 4
  STAGE IIB               13                31
  STAGE III                1                 0
  STAGE IIIA               1                 2
  STAGE IIIB              10                32
  STAGE IVA                4                 3
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   120  44
  3Q GAIN WILD-TYPE  91  23
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              164               114 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               44                23 
$`3Q GAIN MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        23.67        11.44        36.56       144.16       177.04 
TCGA-C5-A1BM TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       82.85        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       57.73        53.16        38.99        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX 
       20.91        40.93         3.58        44.22        73.18        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CJ 
       78.35       100.14        33.24        18.02        17.85       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 
      134.33        15.48       155.77        94.95         9.34         2.73 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       50.99         8.35        23.51         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        63.98        87.75        36.76        55.63        69.96 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       95.67        22.98        16.83        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       40.87        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A439 TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       31.73         7.46        26.79        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM 
       27.22         0.36        12.59         1.51        19.27         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RL TCGA-EK-A2RN 
        0.36         0.13        40.96         4.31        47.77         0.53 
TCGA-EK-A3GM TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A3NI 
        0.76        20.35        15.22        19.79        23.84        20.98 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-GH-A9DA 
        1.48        16.14        28.31        14.01        10.55        17.75 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LA 
       25.41        16.57        21.67        20.78        14.93       137.16 
TCGA-IR-A3LC TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
      129.37        36.36        21.44        20.48        15.58         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 
       18.15       209.59        44.61        20.91        11.28         0.30 
TCGA-LP-A7HU TCGA-MA-AA41 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A913 TCGA-PN-A8MA 
       13.35         8.35        28.08        19.96        17.23         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41        15.95         9.04        17.56        14.07 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC 
       14.60        11.67        93.99        12.16        10.03        46.52 
TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       45.57        23.97        19.96        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       36.13        11.51        59.18        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
        4.73        33.37        40.14        15.68        56.35        55.50 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       51.32        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UU 
       24.30        46.92        45.11        27.25        47.47        14.53 
TCGA-VS-A9UV TCGA-VS-A9V2 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAX4 
        3.42        18.25        15.42        26.01        29.26         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
        1.41         0.16 

$`3Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BL 
       17.52        17.82        57.04        68.84        18.74       173.29 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A2LV TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HL 
        5.46        19.86        73.45        38.43        52.01        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
      210.67       154.32        20.35       147.35        17.19       131.11 
TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
       13.61        45.83       146.86        99.91        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DR-A0ZM TCGA-DS-A7WF TCGA-EA-A3QE TCGA-EA-A3Y4 
       20.91        14.73        58.88        16.18        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 
       26.40        24.56        26.01         0.30        24.82        14.89 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PK 
       24.00        13.48        60.72        26.27         6.64         0.39 
TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.43         1.45         0.10         0.43         0.10         0.49 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        0.03         7.92        14.70         8.32        15.55         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G 
       19.04        16.11        31.36        36.26        26.14        35.44 
TCGA-FU-A770 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH 
        1.12         9.44       147.39        66.81        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A69B 
       81.96        29.85        27.42         3.29        24.56        28.37 
TCGA-JX-A3PZ TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X 
       21.11         0.89        12.49         0.82        22.52        19.56 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A5YI TCGA-MY-A5BD 
       17.82        19.56         8.52        11.38        34.62        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       35.05        20.84        16.14        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PI TCGA-VS-A8EH TCGA-VS-A8QH TCGA-VS-A952 
       22.62        19.59        69.50        32.42        39.78        58.45 
TCGA-VS-A958 TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UQ 
       50.14        27.12         1.71        14.53        47.87        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       26.07        15.85        18.25        67.20        18.84         5.16 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZX-AA5X 
       17.75         4.34        16.24        67.59        19.13         3.91 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.13              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           209.59            210.67 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           25.660            20.615 
[1] "0.1 - 209.6 (25.7)" "0.0 - 210.7 (20.6)"
[1] "hr=" "1.2"
D6V2, continuous
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED   75 45 15  5
  3Q GAIN WILD-TYPE 60 25  6  3
D6V3, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              75                60
  T2              45                25
  T3              15                 6
  T4               5                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   70 41
  3Q GAIN WILD-TYPE 59 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     70   41
  3Q GAIN WILD-TYPE   59   15
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              70                59
  1              41                15
[1] 2 2
[1] FALSE
D6V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   68  6
  3Q GAIN WILD-TYPE 40  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     68    6
  3Q GAIN WILD-TYPE   40    4
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              68                40
  1               6                 4
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   31 76
  3Q GAIN WILD-TYPE 24 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     31   76
  3Q GAIN WILD-TYPE   24   47
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               31                24
  YES              76                47
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED               2                              155
  3Q GAIN WILD-TYPE             4                               87
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3Q GAIN MUTATED                                               3
  3Q GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3Q GAIN MUTATED                                     9
  3Q GAIN WILD-TYPE                                  12
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3Q GAIN MUTATED                                           1
  3Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3Q GAIN MUTATED                                              5
  3Q GAIN WILD-TYPE                                           12
D6V7, multiclass
                                               clus
vv                                              3Q GAIN MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                          155
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                5
                                               clus
vv                                              3Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                             87
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  4    12
  3Q GAIN WILD-TYPE                                4     7
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED                          20
  3Q GAIN WILD-TYPE                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           0   112
  3Q GAIN WILD-TYPE                                         2    90
D6V10, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        4                 4
  ASIAN                                                  12                 7
  BLACK OR AFRICAN AMERICAN                              20                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                 112                90
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   11 94
  3Q GAIN WILD-TYPE 12 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     11   94
  3Q GAIN WILD-TYPE   12   68
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  11                12
  NOT HISPANIC OR LATINO              94                68
[1] 2 2
[1] FALSE
D6V12, continuous
D6V13, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   107  45
  3Q GAIN WILD-TYPE  76  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    107   45
  3Q GAIN WILD-TYPE   76   29
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  TUMOR FREE             107                76
  WITH TUMOR              45                29
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  3Q GAIN MUTATED   10 79 67  0 16
  3Q GAIN WILD-TYPE  8 50 48  1  8
D6V14, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  G1              10                 8
  G2              79                50
  G3              67                48
  G4               0                 1
  GX              16                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, continuous
D6V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3Q GAIN MUTATED                                            22
  3Q GAIN WILD-TYPE                                          16
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  3Q GAIN MUTATED                                        5
  3Q GAIN WILD-TYPE                                      4
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  3Q GAIN MUTATED                                                 3
  3Q GAIN WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3Q GAIN MUTATED               39                  85
  3Q GAIN WILD-TYPE             23                  58
D6V17, multiclass
                                                 clus
vv                                                3Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               3
  CURRENT SMOKER                                               39
  LIFELONG NON-SMOKER                                          85
                                                 clus
vv                                                3Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 23
  LIFELONG NON-SMOKER                                            58
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V18, continuous
D6V19, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   18  2
  3Q GAIN WILD-TYPE  7  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     18    2
  3Q GAIN WILD-TYPE    7    1
                         clus
vv                        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                 18                 7
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
D6V20, continuous
D6V21, continuous
D6V22, continuous
D6V23, continuous
D6V24, continuous
D6V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  3Q GAIN MUTATED                                     1
  3Q GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  3Q GAIN MUTATED                                     5                      27
  3Q GAIN WILD-TYPE                                   2                       9
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3Q GAIN MUTATED                         1                       6
  3Q GAIN WILD-TYPE                       0                       2
D6V26, multiclass
                                     clus
vv                                    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               5                 2
  OTHER LOCATION, SPECIFY                          27                 9
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           6                 2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  3Q GAIN MUTATED                                               2
  3Q GAIN WILD-TYPE                                             0
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  3Q GAIN MUTATED                                               12
  3Q GAIN WILD-TYPE                                             13
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3Q GAIN MUTATED                                                                                  53
  3Q GAIN WILD-TYPE                                                                                29
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3Q GAIN MUTATED                                                                                             71
  3Q GAIN WILD-TYPE                                                                                           50
D6V27, multiclass
                                                                                              clus
vv                                                                                             3Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         53
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              71
                                                                                              clus
vv                                                                                             3Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V28, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   38 47
  3Q GAIN WILD-TYPE 33 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     38   47
  3Q GAIN WILD-TYPE   33   27
         clus
vv        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ABSENT               38                33
  PRESENT              47                27
[1] 2 2
[1] FALSE
D6V29, continuous
D6V30, continuous
D6V31, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   30 67
  3Q GAIN WILD-TYPE 19 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     30   67
  3Q GAIN WILD-TYPE   19   50
                                          clus
vv                                         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  30                19
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              67                50
[1] 2 2
[1] FALSE
D6V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3Q GAIN MUTATED             10          34         47
  3Q GAIN WILD-TYPE            5          20         38
D6V33, multiclass
              clus
vv             3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CURRENT USER              10                 5
  FORMER USER               34                20
  NEVER USED                47                38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V34, continuous
D6V35, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   55 10
  3Q GAIN WILD-TYPE 37  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     55   10
  3Q GAIN WILD-TYPE   37    8
         clus
vv        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ABSENT               55                37
  PRESENT              10                 8
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  3Q GAIN MUTATED             1        64     0
  3Q GAIN WILD-TYPE           4        36     2
D6V36, multiclass
             clus
vv            3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                64                36
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V37, continuous
D6V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  3Q GAIN MUTATED         2        0         0         0       19        47
  3Q GAIN WILD-TYPE       3        1         1         1       15        30
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  3Q GAIN MUTATED          17        4         5          4          4
  3Q GAIN WILD-TYPE        20        0         3          1          3
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  3Q GAIN MUTATED          29         1          3         26         6
  3Q GAIN WILD-TYPE        15         0          0         16         1
                   vv
clus                STAGE IVB
  3Q GAIN MUTATED           4
  3Q GAIN WILD-TYPE         8
D6V39, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                19                15
  STAGE IB1               47                30
  STAGE IB2               17                20
  STAGE II                 4                 0
  STAGE IIA                5                 3
  STAGE IIA1               4                 1
  STAGE IIA2               4                 3
  STAGE IIB               29                15
  STAGE III                1                 0
  STAGE IIIA               3                 0
  STAGE IIIB              26                16
  STAGE IVA                6                 1
  STAGE IVB                4                 8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     8   2
  4P GAIN WILD-TYPE 203  65
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               268 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                65 
$`4P GAIN MUTATED`
TCGA-C5-A1MN TCGA-C5-A7X5 TCGA-C5-A8XI TCGA-EK-A2PI TCGA-FU-A23K TCGA-IR-A3LF 
       40.93        13.61         8.35        19.27         1.22        96.95 
TCGA-JX-A3Q8 TCGA-LP-A5U3 TCGA-R2-A69V TCGA-ZJ-AAX4 
       44.61         0.82        19.59         0.69 

$`4P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       30.21        35.01        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91         3.58        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       52.01        18.02        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC 
      155.77       131.11        94.95         9.34         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83       146.86        99.91        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91        14.73         1.12        95.11        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63        69.96 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       95.67        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
        0.36        12.59        60.72        26.27         6.64         1.51 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
       40.96         4.31         0.10         0.43        47.77         0.53 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.49         0.76         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L 
       15.22        14.70        19.79         8.32        15.55        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12        17.75        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       18.15        21.11       209.59        20.91        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
       12.49         0.30        13.35        22.52        19.56        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         8.35         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
       19.96        54.81        35.05        20.84        17.23         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 
       14.07        15.88         9.34        18.64        22.62        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        69.50        10.03        46.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       45.57        32.42        23.97        19.96        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       53.59        36.13        11.51        59.18        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       40.87        16.64         4.73        33.37        40.14        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       15.68        56.35        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       43.40        48.39        28.50        29.95        27.12        24.30 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       46.92        45.11         1.71        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
        4.34        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         1.41         0.16         3.91 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.69              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            96.95            210.67 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           16.440            23.755 
[1] "0.7 - 97.0 (16.4)"  "0.0 - 210.7 (23.8)"
[1] "hr=" "1.1"
D7V2, continuous
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     6   1   0   0
  4P GAIN WILD-TYPE 129  69  21   8
D7V3, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               6               129
  T2               1                69
  T3               0                21
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6   1
  4P GAIN WILD-TYPE 123  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    1
  4P GAIN WILD-TYPE  123   55
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               6               123
  1               1                55
[1] 2 2
[1] FALSE
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   0
  4P GAIN WILD-TYPE 104  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    0
  4P GAIN WILD-TYPE  104   10
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               4               104
  1               0                10
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     2   4
  4P GAIN WILD-TYPE  53 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    4
  4P GAIN WILD-TYPE   53  119
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                2                53
  YES               4               119
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED               0                                9
  4P GAIN WILD-TYPE             6                              233
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4P GAIN MUTATED                                               1
  4P GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4P GAIN MUTATED                                     1
  4P GAIN WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4P GAIN MUTATED                                           0
  4P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4P GAIN MUTATED                                              0
  4P GAIN WILD-TYPE                                           17
D7V7, multiclass
                                               clus
vv                                              4P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            9
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              4P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            233
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     2
  4P GAIN WILD-TYPE                                8    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED                           2
  4P GAIN WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0     6
  4P GAIN WILD-TYPE                                         2   196
D7V10, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               2                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                   6               196
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   6
  4P GAIN WILD-TYPE  23 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    6
  4P GAIN WILD-TYPE   23  156
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                23
  NOT HISPANIC OR LATINO               6               156
[1] 2 2
[1] FALSE
D7V12, continuous
D7V13, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6   2
  4P GAIN WILD-TYPE 177  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    2
  4P GAIN WILD-TYPE  177   72
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  TUMOR FREE               6               177
  WITH TUMOR               2                72
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  4P GAIN MUTATED     0   3   7   0   0
  4P GAIN WILD-TYPE  18 126 108   1  24
D7V14, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  G1               0                18
  G2               3               126
  G3               7               108
  G4               0                 1
  GX               0                24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                42 
       TCGA-2W-A8YY        TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BQ        TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A7CM        TCGA-C5-A7CO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A8XH        TCGA-C5-A907        TCGA-DG-A2KK        TCGA-DS-A3LQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EK-A2RA        TCGA-EX-A69M        TCGA-FU-A2QG        TCGA-FU-A3TX 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-HM-A3JK        TCGA-HM-A4S6        TCGA-IR-A3L7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JX-A3Q0        TCGA-MA-AA43 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-Q1-A73S 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-RA-A741        TCGA-VS-A8QF        TCGA-VS-A94Z        TCGA-VS-A9V0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-VS-A9V4        TCGA-WL-A834        TCGA-ZJ-A8QR        TCGA-ZJ-AAXA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ZJ-AAXT        TCGA-ZJ-AB0I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4P GAIN MUTATED                                             1
  4P GAIN WILD-TYPE                                          37
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  4P GAIN MUTATED                                        0
  4P GAIN WILD-TYPE                                      9
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  4P GAIN MUTATED                                                 0
  4P GAIN WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4P GAIN MUTATED                2                   5
  4P GAIN WILD-TYPE             60                 138
D7V17, multiclass
                                                 clus
vv                                                4P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                2
  LIFELONG NON-SMOKER                                           5
                                                 clus
vv                                                4P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    37
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 60
  LIFELONG NON-SMOKER                                           138
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V18, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                82 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A2LS        TCGA-C5-A2LT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7X8        TCGA-C5-A8YQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A8YT        TCGA-C5-A8ZZ        TCGA-C5-A907        TCGA-DG-A2KK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-EA-A556        TCGA-EK-A2RA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A5XV        TCGA-FU-A770        TCGA-GH-A9DA        TCGA-HM-A4S6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-JW-AAVH        TCGA-JX-A3Q0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MA-AA3W        TCGA-MA-AA3X        TCGA-MA-AA41        TCGA-MA-AA43 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-Q1-A73Q 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-Q1-A73S        TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-VS-A8EH        TCGA-VS-A8QF        TCGA-VS-A8QM        TCGA-VS-A94Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-VS-A94Z        TCGA-VS-A9UP        TCGA-VS-A9UU        TCGA-VS-A9V0 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-VS-A9V1        TCGA-VS-A9V4        TCGA-WL-A834        TCGA-ZJ-A8QQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ZJ-A8QR        TCGA-ZJ-AAXA        TCGA-ZJ-AAXN        TCGA-ZJ-AAXT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ZJ-AAXU        TCGA-ZJ-AB0I 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V19, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  0
  4P GAIN WILD-TYPE 24  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    0
  4P GAIN WILD-TYPE   24    3
                         clus
vv                        4P GAIN MUTATED 4P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  1                24
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D7V20, continuous
D7V21, continuous
D7V22, continuous
D7V23, continuous
D7V24, continuous
D7V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  4P GAIN MUTATED                                     0
  4P GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  4P GAIN MUTATED                                     0                       1
  4P GAIN WILD-TYPE                                   7                      35
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4P GAIN MUTATED                         0                       1
  4P GAIN WILD-TYPE                       1                       7
D7V26, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                53 
       TCGA-2W-A8YY        TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BK        TCGA-C5-A1BM        TCGA-C5-A1M5        TCGA-C5-A1M7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME        TCGA-C5-A1MF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MJ        TCGA-C5-A1MP        TCGA-C5-A2LS        TCGA-C5-A2LT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2M1        TCGA-C5-A3HE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CJ        TCGA-C5-A7UC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-C5-A7XC        TCGA-C5-A8XH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DG-A2KK        TCGA-DG-A2KL        TCGA-DR-A0ZM        TCGA-DS-A0VK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A3LQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A50E        TCGA-EK-A2RN        TCGA-EK-A2RO        TCGA-EX-A1H5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EX-A449        TCGA-FU-A3EO        TCGA-HM-A4S6        TCGA-IR-A3LH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LI        TCGA-IR-A3LK        TCGA-MU-A51Y        TCGA-MU-A8JM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-VS-A8QA        TCGA-VS-A9UT        TCGA-WL-A834 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-XS-A8TJ 
"4P GAIN WILD-TYPE" 
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  4P GAIN MUTATED                                               0
  4P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  4P GAIN MUTATED                                                1
  4P GAIN WILD-TYPE                                             24
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4P GAIN MUTATED                                                                                   2
  4P GAIN WILD-TYPE                                                                                80
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4P GAIN MUTATED                                                                                              4
  4P GAIN WILD-TYPE                                                                                          117
D7V27, multiclass
                                                                                              clus
vv                                                                                             4P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               4
                                                                                              clus
vv                                                                                             4P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           80
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V28, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    3  3
  4P GAIN WILD-TYPE 68 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3    3
  4P GAIN WILD-TYPE   68   71
         clus
vv        4P GAIN MUTATED 4P GAIN WILD-TYPE
  ABSENT                3                68
  PRESENT               3                71
[1] 2 2
[1] FALSE
D7V29, continuous
D7V30, continuous
D7V31, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     2   6
  4P GAIN WILD-TYPE  47 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    6
  4P GAIN WILD-TYPE   47  111
                                          clus
vv                                         4P GAIN MUTATED 4P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   2                47
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               6               111
[1] 2 2
[1] FALSE
D7V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4P GAIN MUTATED              0           2          3
  4P GAIN WILD-TYPE           15          52         82
D7V33, multiclass
              clus
vv             4P GAIN MUTATED 4P GAIN WILD-TYPE
  CURRENT USER               0                15
  FORMER USER                2                52
  NEVER USED                 3                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V34, continuous
D7V35, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    4  0
  4P GAIN WILD-TYPE 88 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    0
  4P GAIN WILD-TYPE   88   18
         clus
vv        4P GAIN MUTATED 4P GAIN WILD-TYPE
  ABSENT                4                88
  PRESENT               0                18
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  4P GAIN MUTATED             1         2     0
  4P GAIN WILD-TYPE           4        98     2
D7V36, multiclass
             clus
vv            4P GAIN MUTATED 4P GAIN WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                 2                98
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V37, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                15 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42        TCGA-MU-A51Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  4P GAIN MUTATED         0        0         0         0        1         3
  4P GAIN WILD-TYPE       5        1         1         1       33        74
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  4P GAIN MUTATED           1        1         0          0          0
  4P GAIN WILD-TYPE        36        3         8          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  4P GAIN MUTATED           0         0          0          3         0
  4P GAIN WILD-TYPE        44         1          3         39         7
                   vv
clus                STAGE IVB
  4P GAIN MUTATED           1
  4P GAIN WILD-TYPE        11
D7V39, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 1                33
  STAGE IB1                3                74
  STAGE IB2                1                36
  STAGE II                 1                 3
  STAGE IIA                0                 8
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                0                44
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               3                39
  STAGE IVA                0                 7
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    13   1
  4Q GAIN WILD-TYPE 198  66
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               264 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                66 
$`4Q GAIN MUTATED`
TCGA-C5-A1MP TCGA-C5-A7XC TCGA-C5-A8XI TCGA-EK-A2PI TCGA-EK-A3GK TCGA-FU-A23K 
        3.58        50.99         8.35        19.27         0.49         1.22 
TCGA-IR-A3LF TCGA-JX-A3Q8 TCGA-LP-A5U3 TCGA-MA-AA41 TCGA-MY-A5BF TCGA-R2-A69V 
       96.95        44.61         0.82         8.35        20.84        19.59 
TCGA-VS-A8QC TCGA-ZJ-AAX4 
       11.51         0.69 

$`4Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       30.21        35.01        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91        40.93        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       52.01        18.02        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
      155.77       131.11        94.95         9.34        13.61         2.73 
TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83       146.86        99.91        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91        14.73         1.12        95.11        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63        69.96 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       95.67        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
        0.36        12.59        60.72        26.27         6.64         1.51 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
       40.96         4.31         0.10         0.43        47.77         0.53 
TCGA-EK-A3GJ TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.76         0.03        20.35         7.92        15.22 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A2QG 
       14.70        19.79         8.32        15.55        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
       16.11        31.36        36.26        20.98        26.14         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       17.75        25.41        16.57        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH 
        9.44       147.39       137.16        66.81       129.37        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        20.91        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.30        13.35        22.52        19.56        17.82        19.56 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       35.05        17.23         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       18.64        22.62        14.60        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       69.50        10.03        46.52        45.57        32.42        23.97 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF 
       19.96        65.49        32.15        53.59        36.13        59.18 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78        31.27        40.87        16.64         4.73        33.37 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       40.14        58.45        15.68        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       51.32        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       27.12        24.30        46.92        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       14.53         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
       18.25        17.75         4.34        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26        67.59        19.13         1.41         0.16         3.91 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.49              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            96.95            210.67 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            9.930            23.985 
[1] "0.5 - 97.0 (9.9)"   "0.0 - 210.7 (24.0)"
[1] "hr=" "2.1"
D8V2, continuous
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     9   3   1   0
  4Q GAIN WILD-TYPE 126  67  20   8
D8V3, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               9               126
  T2               3                67
  T3               1                20
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     9   4
  4Q GAIN WILD-TYPE 120  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      9    4
  4Q GAIN WILD-TYPE  120   52
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               9               120
  1               4                52
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     6   1
  4Q GAIN WILD-TYPE 102   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      6    1
  4Q GAIN WILD-TYPE  102    9
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               6               102
  1               1                 9
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   5
  4Q GAIN WILD-TYPE  51 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    5
  4Q GAIN WILD-TYPE   51  118
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                4                51
  YES               5               118
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED               0                               13
  4Q GAIN WILD-TYPE             6                              229
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4Q GAIN MUTATED                                               1
  4Q GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4Q GAIN MUTATED                                     2
  4Q GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4Q GAIN MUTATED                                           0
  4Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4Q GAIN MUTATED                                              0
  4Q GAIN WILD-TYPE                                           17
D8V7, multiclass
                                               clus
vv                                              4Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           13
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              4Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            229
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     2
  4Q GAIN WILD-TYPE                                8    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED                           2
  4Q GAIN WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0    10
  4Q GAIN WILD-TYPE                                         2   192
D8V10, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               2                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  10               192
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   8
  4Q GAIN WILD-TYPE  22 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    8
  4Q GAIN WILD-TYPE   22  154
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                22
  NOT HISPANIC OR LATINO               8               154
[1] 2 2
[1] FALSE
D8V12, continuous
D8V13, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     8   3
  4Q GAIN WILD-TYPE 175  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      8    3
  4Q GAIN WILD-TYPE  175   71
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  TUMOR FREE               8               175
  WITH TUMOR               3                71
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  4Q GAIN MUTATED     1   5   8   0   0
  4Q GAIN WILD-TYPE  17 124 107   1  24
D8V14, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  G1               1                17
  G2               5               124
  G3               8               107
  G4               0                 1
  GX               0                24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                42 
       TCGA-2W-A8YY        TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BQ        TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A7CM        TCGA-C5-A7CO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A8XH        TCGA-C5-A907        TCGA-DG-A2KK        TCGA-DS-A3LQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EK-A2RA        TCGA-EX-A69M        TCGA-FU-A2QG        TCGA-FU-A3TX 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-HM-A3JK        TCGA-HM-A4S6        TCGA-IR-A3L7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JX-A3Q0        TCGA-MA-AA43 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-Q1-A73S 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-RA-A741        TCGA-VS-A8QF        TCGA-VS-A94Z        TCGA-VS-A9V0 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-VS-A9V4        TCGA-WL-A834        TCGA-ZJ-A8QR        TCGA-ZJ-AAXA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ZJ-AAXT        TCGA-ZJ-AB0I 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4Q GAIN MUTATED                                             1
  4Q GAIN WILD-TYPE                                          37
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  4Q GAIN MUTATED                                        0
  4Q GAIN WILD-TYPE                                      9
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  4Q GAIN MUTATED                                                 0
  4Q GAIN WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4Q GAIN MUTATED                4                   7
  4Q GAIN WILD-TYPE             58                 136
D8V17, multiclass
                                                 clus
vv                                                4Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                4
  LIFELONG NON-SMOKER                                           7
                                                 clus
vv                                                4Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    37
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 58
  LIFELONG NON-SMOKER                                           136
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V18, continuous
D8V19, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  0
  4Q GAIN WILD-TYPE 25  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    0
  4Q GAIN WILD-TYPE   25    3
D8V20, continuous
D8V21, continuous
D8V22, continuous
D8V23, continuous
D8V24, continuous
D8V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  4Q GAIN MUTATED                                     0
  4Q GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  4Q GAIN MUTATED                                     0                       3
  4Q GAIN WILD-TYPE                                   7                      33
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4Q GAIN MUTATED                         0                       1
  4Q GAIN WILD-TYPE                       1                       7
D8V26, multiclass
                                     clus
vv                                    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           3                33
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  4Q GAIN MUTATED                                               0
  4Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  4Q GAIN MUTATED                                                2
  4Q GAIN WILD-TYPE                                             23
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4Q GAIN MUTATED                                                                                   3
  4Q GAIN WILD-TYPE                                                                                79
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4Q GAIN MUTATED                                                                                              5
  4Q GAIN WILD-TYPE                                                                                          116
D8V27, multiclass
                                                                                              clus
vv                                                                                             4Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               5
                                                                                              clus
vv                                                                                             4Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           79
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V28, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    3  6
  4Q GAIN WILD-TYPE 68 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    6
  4Q GAIN WILD-TYPE   68   68
         clus
vv        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ABSENT                3                68
  PRESENT               6                68
[1] 2 2
[1] FALSE
D8V29, continuous
D8V30, continuous
D8V31, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   8
  4Q GAIN WILD-TYPE  49 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    8
  4Q GAIN WILD-TYPE   49  109
                                          clus
vv                                         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   0                49
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               8               109
[1] 2 2
[1] FALSE
D8V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4Q GAIN MUTATED              1           2          3
  4Q GAIN WILD-TYPE           14          52         82
D8V33, multiclass
              clus
vv             4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CURRENT USER               1                14
  FORMER USER                2                52
  NEVER USED                 3                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V34, continuous
D8V35, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    5  0
  4Q GAIN WILD-TYPE 87 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5    0
  4Q GAIN WILD-TYPE   87   18
         clus
vv        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ABSENT                5                87
  PRESENT               0                18
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  4Q GAIN MUTATED             0         3     0
  4Q GAIN WILD-TYPE           5        97     2
D8V36, multiclass
             clus
vv            4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                 3                97
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V37, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                15 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42        TCGA-MU-A51Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  4Q GAIN MUTATED         0        0         0         0        1         5
  4Q GAIN WILD-TYPE       5        1         1         1       33        72
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  4Q GAIN MUTATED           2        1         0          0          1
  4Q GAIN WILD-TYPE        35        3         8          5          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  4Q GAIN MUTATED           1         0          0          3         1
  4Q GAIN WILD-TYPE        43         1          3         39         6
                   vv
clus                STAGE IVB
  4Q GAIN MUTATED           0
  4Q GAIN WILD-TYPE        12
D8V39, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 1                33
  STAGE IB1                5                72
  STAGE IB2                2                35
  STAGE II                 1                 3
  STAGE IIA                0                 8
  STAGE IIA1               0                 5
  STAGE IIA2               1                 6
  STAGE IIB                1                43
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               3                39
  STAGE IVA                1                 6
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    79  24
  5P GAIN WILD-TYPE 132  43
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              103               175 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               24                43 
$`5P GAIN MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BJ TCGA-C5-A1BQ TCGA-C5-A1M6 
       17.82        49.48        57.04       144.16        19.86        31.40 
TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT 
       46.32        57.73        20.91        40.93         3.58        73.18 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7CM 
      100.14        38.43        52.01        18.02        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC 
      147.35       155.77       131.11         9.34         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A907 TCGA-DG-A2KH 
       45.83       146.86        99.91        27.52        14.73         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A3HR TCGA-EA-A3Y4 
       95.11        44.94        22.98        39.55        30.90        36.89 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2PG TCGA-EK-A2PI 
       31.73        26.01        25.91        27.22         1.51        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RA TCGA-EK-A2RN TCGA-EK-A3GK 
        0.39         0.43         0.59        40.96         0.53         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF 
        0.76         0.03        20.35        15.22        19.79        15.55 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ 
       23.84        20.98        10.55        17.75        25.41        21.67 
TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A852 
       78.71        29.85        36.36        27.42        24.56         8.28 
TCGA-JW-AAVH TCGA-JX-A5QV TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 
       18.15        20.91        22.52        17.82        19.56         8.52 
TCGA-MA-AA43 TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       11.38        35.05         2.96        16.41        15.95         9.04 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8QC 
       12.16        69.50        23.97        19.96        65.49        11.51 
TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A958 
       59.18        16.64         4.73        40.14        15.68        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       51.32        50.47        28.50        29.95        27.12        24.30 
TCGA-VS-A9UH TCGA-VS-A9UL TCGA-VS-A9UY TCGA-VS-A9V4 TCGA-WL-A834 TCGA-XS-A8TJ 
       46.92        14.53        18.25         4.34        26.01        29.26 
TCGA-ZJ-AAXU 
        0.16 

$`5P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       17.52        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M8 
      177.04       173.29        82.85         5.46        67.46        30.21 
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       35.01        53.16        38.99        35.61         0.46         2.43 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HF 
       44.22        73.45        83.05        78.35        33.24        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7UC 
       20.42       210.67       154.32       101.82       134.33        17.19 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ 
       94.95        13.61         8.35        23.51        20.81        20.91 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       82.06        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       69.96        95.67        16.83        16.18        17.52         8.28 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       40.87        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       26.40        24.56         0.30        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       26.79        27.29        27.25        24.00        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2R8 
       12.59        60.72        26.27         6.64         0.36         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ 
        0.13         4.31         0.10         0.43        47.77         0.10 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92        14.70         8.32         1.22        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36        36.26        26.14         1.48        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
       14.01        35.44         1.12        16.57        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LI TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       81.96         3.29        21.44        20.48        15.58        28.37 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        44.61        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA41 TCGA-MU-A51Y 
        0.30         0.82        13.35        19.56         8.35        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 
       34.62        19.96        54.81        20.84        17.23        15.58 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EB 
       22.62        19.59        14.60        11.67        93.99        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       46.52        45.57        32.42        32.15        53.59        36.13 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 
       39.78        31.27        40.87        33.37        58.45        56.35 
TCGA-VS-A957 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM 
       55.50        43.40        48.39        45.11         1.71        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       47.87        47.47        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
        3.42        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       16.24        15.42        67.59        19.13         0.69         1.41 
TCGA-ZX-AA5X 
        3.91 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           155.77            210.67 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            23.84             22.62 
[1] "0.0 - 155.8 (23.8)" "0.1 - 210.7 (22.6)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED   41 30 11  3
  5P GAIN WILD-TYPE 94 40 10  5
D9V3, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              41                94
  T2              30                40
  T3              11                10
  T4               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   44 19
  5P GAIN WILD-TYPE 85 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     44   19
  5P GAIN WILD-TYPE   85   37
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              44                85
  1              19                37
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   45  1
  5P GAIN WILD-TYPE 63  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     45    1
  5P GAIN WILD-TYPE   63    9
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              45                63
  1               1                 9
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   18 53
  5P GAIN WILD-TYPE 37 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     18   53
  5P GAIN WILD-TYPE   37   70
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               18                37
  YES              53                70
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED               1                              103
  5P GAIN WILD-TYPE             5                              139
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5P GAIN MUTATED                                               2
  5P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5P GAIN MUTATED                                     4
  5P GAIN WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5P GAIN MUTATED                                           1
  5P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5P GAIN MUTATED                                              2
  5P GAIN WILD-TYPE                                           15
D9V7, multiclass
                                               clus
vv                                              5P GAIN MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                          103
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              5P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            139
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  2     4
  5P GAIN WILD-TYPE                                6    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED                          12
  5P GAIN WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           0    79
  5P GAIN WILD-TYPE                                         2   123
D9V10, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 6
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                              12                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  79               123
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    13  54
  5P GAIN WILD-TYPE  10 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     13   54
  5P GAIN WILD-TYPE   10  108
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  13                10
  NOT HISPANIC OR LATINO              54               108
[1] 2 2
[1] FALSE
D9V12, continuous
D9V13, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    66  29
  5P GAIN WILD-TYPE 117  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     66   29
  5P GAIN WILD-TYPE  117   45
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  TUMOR FREE              66               117
  WITH TUMOR              29                45
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  5P GAIN MUTATED    4 43 51  1  7
  5P GAIN WILD-TYPE 14 86 64  0 17
D9V14, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  G1               4                14
  G2              43                86
  G3              51                64
  G4               1                 0
  GX               7                17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, continuous
D9V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5P GAIN MUTATED                                            16
  5P GAIN WILD-TYPE                                          22
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  5P GAIN MUTATED                                        2
  5P GAIN WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  5P GAIN MUTATED                                                 1
  5P GAIN WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5P GAIN MUTATED               24                  52
  5P GAIN WILD-TYPE             38                  91
D9V17, multiclass
                                                 clus
vv                                                5P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               24
  LIFELONG NON-SMOKER                                          52
                                                 clus
vv                                                5P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 38
  LIFELONG NON-SMOKER                                            91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V18, continuous
D9V19, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    9  0
  5P GAIN WILD-TYPE 16  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      9    0
  5P GAIN WILD-TYPE   16    3
                         clus
vv                        5P GAIN MUTATED 5P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  9                16
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D9V20, continuous
D9V21, continuous
D9V22, continuous
D9V23, continuous
D9V24, continuous
D9V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  5P GAIN MUTATED                                     0
  5P GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  5P GAIN MUTATED                                     3                      12
  5P GAIN WILD-TYPE                                   4                      24
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5P GAIN MUTATED                         0                       2
  5P GAIN WILD-TYPE                       1                       6
D9V26, multiclass
                                     clus
vv                                    5P GAIN MUTATED 5P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               3                 4
  OTHER LOCATION, SPECIFY                          12                24
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  5P GAIN MUTATED                                               0
  5P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5P GAIN MUTATED                                                5
  5P GAIN WILD-TYPE                                             20
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5P GAIN MUTATED                                                                                  31
  5P GAIN WILD-TYPE                                                                                51
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5P GAIN MUTATED                                                                                             41
  5P GAIN WILD-TYPE                                                                                           80
D9V27, multiclass
                                                                                              clus
vv                                                                                             5P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         31
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              41
                                                                                              clus
vv                                                                                             5P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V28, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   22 21
  5P GAIN WILD-TYPE 49 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     22   21
  5P GAIN WILD-TYPE   49   53
         clus
vv        5P GAIN MUTATED 5P GAIN WILD-TYPE
  ABSENT               22                49
  PRESENT              21                53
[1] 2 2
[1] FALSE
D9V29, continuous
D9V30, continuous
D9V31, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   16 49
  5P GAIN WILD-TYPE 33 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     16   49
  5P GAIN WILD-TYPE   33   68
                                          clus
vv                                         5P GAIN MUTATED 5P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  16                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              49                68
[1] 2 2
[1] FALSE
D9V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5P GAIN MUTATED              4          19         27
  5P GAIN WILD-TYPE           11          35         58
D9V33, multiclass
              clus
vv             5P GAIN MUTATED 5P GAIN WILD-TYPE
  CURRENT USER               4                11
  FORMER USER               19                35
  NEVER USED                27                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V34, continuous
D9V35, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   26  6
  5P GAIN WILD-TYPE 66 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     26    6
  5P GAIN WILD-TYPE   66   12
         clus
vv        5P GAIN MUTATED 5P GAIN WILD-TYPE
  ABSENT               26                66
  PRESENT               6                12
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  5P GAIN MUTATED             0        42     0
  5P GAIN WILD-TYPE           5        58     2
D9V36, multiclass
             clus
vv            5P GAIN MUTATED 5P GAIN WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                42                58
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V37, continuous
D9V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  5P GAIN MUTATED         1        0         0         0        7        26
  5P GAIN WILD-TYPE       4        1         1         1       27        51
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  5P GAIN MUTATED          14        1         3          4          1
  5P GAIN WILD-TYPE        23        3         5          1          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  5P GAIN MUTATED          24         0          3         19         4
  5P GAIN WILD-TYPE        20         1          0         23         3
                   vv
clus                STAGE IVB
  5P GAIN MUTATED           1
  5P GAIN WILD-TYPE        11
D9V39, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 7                27
  STAGE IB1               26                51
  STAGE IB2               14                23
  STAGE II                 1                 3
  STAGE IIA                3                 5
  STAGE IIA1               4                 1
  STAGE IIA2               1                 6
  STAGE IIB               24                20
  STAGE III                0                 1
  STAGE IIIA               3                 0
  STAGE IIIB              19                23
  STAGE IVA                4                 3
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    33   8
  5Q GAIN WILD-TYPE 178  59
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               41               237 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                59 
$`5Q GAIN MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A7CM 
       31.40        46.32        57.73        20.91        40.93        20.35 
TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8YR TCGA-DG-A2KH 
      147.35       131.11         2.73        50.99        27.52         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-EA-A1QS TCGA-EA-A5O9 TCGA-EK-A2PG TCGA-EK-A2PK 
       95.11        44.94        39.55        25.91         1.51         0.39 
TCGA-EK-A2PM TCGA-EK-A2RN TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 
        0.59         0.53         0.76         0.03        20.35        15.22 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-GH-A9DA TCGA-IR-A3LK TCGA-IR-A3LL TCGA-MA-AA43 
       19.79        15.55        17.75        29.85        36.36        11.38 
TCGA-MY-A5BE TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-UC-A7PG TCGA-VS-A8EI 
       35.05        16.41        15.95         9.04        12.16        23.97 
TCGA-VS-A953 TCGA-VS-A958 TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       15.68        50.14        27.12        24.30        46.92 

$`5Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 
       82.85         5.46        19.86        67.46        30.21        35.01 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP 
       53.16        38.99        35.61         0.46         2.43         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UC 
      210.67       154.32       101.82       134.33        15.48        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XH TCGA-C5-A8XI 
      155.77        94.95         9.34        13.61        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
      146.86        99.91        23.51        20.81        20.91        14.73 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       82.06        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       69.96        95.67        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       27.29        27.25        27.22        24.00        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL 
       12.59        60.72        26.27         6.64        19.27         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.36         1.45         0.13        40.96         4.31         0.10 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H6 TCGA-EX-A449 
        0.43        47.77         0.10         0.49         7.92        14.70 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        8.32         1.22        23.84        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26        20.98        26.14         1.48        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC 
       14.01        35.44        10.55         1.12        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VG 
       66.81       129.37        96.95        78.71        81.96        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        8.28        18.15        21.11       209.59        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        19.56        17.82        19.56         8.35         8.52 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 
       28.08        34.62        19.96        54.81        20.84        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
        2.96        15.58        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       19.96        65.49        32.15        53.59        36.13        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       59.18        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A959 
       33.37        40.14        58.45        56.35        55.50        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UI 
       50.47        43.40        48.39        28.50        29.95        45.11 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
        1.71        14.53        27.25        47.87        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       26.07        15.85        14.53         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.84         5.16        18.25        17.75         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           147.35            210.67 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            20.91             23.51 
[1] "0.0 - 147.3 (20.9)" "0.1 - 210.7 (23.5)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED    14   8   6   2
  5Q GAIN WILD-TYPE 121  62  15   6
D10V3, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              14               121
  T2               8                62
  T3               6                15
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    17   6
  5Q GAIN WILD-TYPE 112  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     17    6
  5Q GAIN WILD-TYPE  112   50
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              17               112
  1               6                50
[1] 2 2
[1] FALSE
D10V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   18  0
  5Q GAIN WILD-TYPE 90 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     18    0
  5Q GAIN WILD-TYPE   90   10
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              18                90
  1               0                10
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     6  19
  5Q GAIN WILD-TYPE  49 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      6   19
  5Q GAIN WILD-TYPE   49  104
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                6                49
  YES              19               104
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED               1                               38
  5Q GAIN WILD-TYPE             5                              204
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5Q GAIN MUTATED                                               2
  5Q GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5Q GAIN MUTATED                                     2
  5Q GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5Q GAIN MUTATED                                           0
  5Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5Q GAIN MUTATED                                              1
  5Q GAIN WILD-TYPE                                           16
D10V7, multiclass
                                               clus
vv                                              5Q GAIN MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              5Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            204
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
D10V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                8    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED                           4
  5Q GAIN WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    32
  5Q GAIN WILD-TYPE                                         2   170
D10V10, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               4                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  32               170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3  21
  5Q GAIN WILD-TYPE  20 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   21
  5Q GAIN WILD-TYPE   20  141
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                20
  NOT HISPANIC OR LATINO              21               141
[1] 2 2
[1] FALSE
D10V12, continuous
D10V13, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    25  10
  5Q GAIN WILD-TYPE 158  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     25   10
  5Q GAIN WILD-TYPE  158   64
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  TUMOR FREE              25               158
  WITH TUMOR              10                64
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  5Q GAIN MUTATED     3  16  19   0   5
  5Q GAIN WILD-TYPE  15 113  96   1  19
D10V14, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  G1               3                15
  G2              16               113
  G3              19                96
  G4               0                 1
  GX               5                19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, continuous
D10V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5Q GAIN MUTATED                                             4
  5Q GAIN WILD-TYPE                                          34
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  5Q GAIN MUTATED                                        1
  5Q GAIN WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  5Q GAIN MUTATED                                                 0
  5Q GAIN WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5Q GAIN MUTATED                9                  22
  5Q GAIN WILD-TYPE             53                 121
D10V17, multiclass
                                                 clus
vv                                                5Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                9
  LIFELONG NON-SMOKER                                          22
                                                 clus
vv                                                5Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    34
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 53
  LIFELONG NON-SMOKER                                           121
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V18, continuous
D10V19, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    4  0
  5Q GAIN WILD-TYPE 21  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    0
  5Q GAIN WILD-TYPE   21    3
                         clus
vv                        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  4                21
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D10V20, continuous
D10V21, continuous
D10V22, continuous
D10V23, continuous
D10V24, continuous
D10V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  5Q GAIN MUTATED                                     0
  5Q GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  5Q GAIN MUTATED                                     2                       5
  5Q GAIN WILD-TYPE                                   5                      31
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5Q GAIN MUTATED                         0                       1
  5Q GAIN WILD-TYPE                       1                       7
D10V26, multiclass
                                     clus
vv                                    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 5
  OTHER LOCATION, SPECIFY                           5                31
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  5Q GAIN MUTATED                                               0
  5Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5Q GAIN MUTATED                                                2
  5Q GAIN WILD-TYPE                                             23
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5Q GAIN MUTATED                                                                                  18
  5Q GAIN WILD-TYPE                                                                                64
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5Q GAIN MUTATED                                                                                             11
  5Q GAIN WILD-TYPE                                                                                          110
D10V27, multiclass
                                                                                              clus
vv                                                                                             5Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              11
                                                                                              clus
vv                                                                                             5Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V28, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   10  7
  5Q GAIN WILD-TYPE 61 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     10    7
  5Q GAIN WILD-TYPE   61   67
         clus
vv        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ABSENT               10                61
  PRESENT               7                67
[1] 2 2
[1] FALSE
D10V29, continuous
D10V30, continuous
D10V31, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    5 18
  5Q GAIN WILD-TYPE 44 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5   18
  5Q GAIN WILD-TYPE   44   99
                                          clus
vv                                         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              18                99
[1] 2 2
[1] FALSE
D10V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5Q GAIN MUTATED              1           6         13
  5Q GAIN WILD-TYPE           14          48         72
D10V33, multiclass
              clus
vv             5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CURRENT USER               1                14
  FORMER USER                6                48
  NEVER USED                13                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V34, continuous
D10V35, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   14  0
  5Q GAIN WILD-TYPE 78 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     14    0
  5Q GAIN WILD-TYPE   78   18
         clus
vv        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ABSENT               14                78
  PRESENT               0                18
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  5Q GAIN MUTATED             0        15     0
  5Q GAIN WILD-TYPE           5        85     2
D10V36, multiclass
             clus
vv            5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                15                85
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V37, continuous
D10V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  5Q GAIN MUTATED         1        0         0         0        2        12
  5Q GAIN WILD-TYPE       4        1         1         1       32        65
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  5Q GAIN MUTATED           6        0         2          1          0
  5Q GAIN WILD-TYPE        31        4         6          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  5Q GAIN MUTATED           6         0          1          8         2
  5Q GAIN WILD-TYPE        38         1          2         34         5
                   vv
clus                STAGE IVB
  5Q GAIN MUTATED           0
  5Q GAIN WILD-TYPE        12
D10V39, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 2                32
  STAGE IB1               12                65
  STAGE IB2                6                31
  STAGE II                 0                 4
  STAGE IIA                2                 6
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                6                38
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               8                34
  STAGE IVA                2                 5
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    35  17
  6P GAIN WILD-TYPE 176  50
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               52               226 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               17                50 
$`6P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MH 
       57.04         5.46        31.40        46.32        35.01        38.99 
TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CH 
       35.61        20.91        78.35        52.01        17.85       154.32 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-DS-A7WI TCGA-EA-A1QS 
      155.77        94.95         2.73        45.83         8.28        39.55 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2PK TCGA-EK-A2PM 
       31.73        26.01        27.22         0.36         0.39         0.59 
TCGA-EK-A2RA TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A57G TCGA-HG-A2PA TCGA-IR-A3LF 
       40.96         1.22        23.84        35.44        25.41        96.95 
TCGA-IR-A3LH TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MA-AA3Y 
       78.71        28.37        44.61        11.28        12.49        17.82 
TCGA-MA-AA43 TCGA-MU-A5YI TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-UC-A7PD 
       11.38        34.62        17.23         2.96        16.41        11.67 
TCGA-VS-A8EJ TCGA-VS-A8QH TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A959 TCGA-VS-A9UD 
       19.96        39.78        58.45        15.68        51.32        24.30 
TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UO TCGA-ZJ-AAXA 
       45.11        14.53        47.87         1.41 

$`6P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ 
       19.86        67.46        30.21        57.73        53.16         0.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        2.43        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HL 
       83.05       100.14        38.43        33.24        18.02        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      210.67       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI 
       17.19       131.11         9.34        13.61        50.99         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
      146.86        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       14.73         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76        55.63        69.96        95.67 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HQ 
       22.98        16.83        16.18        17.52        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       26.40        24.56         0.30        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
       26.79        25.91        27.29        27.25        24.00        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        60.72        26.27         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RD 
        0.43         0.36         1.45         0.13         4.31         0.10 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM 
        0.43        47.77         0.53         0.10         0.49         0.76 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92        15.22        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        8.32        15.55        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       20.98        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
       10.55         1.12        17.75        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       21.44        20.48        15.58         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
      209.59        20.91         0.89         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y 
       22.52        19.56        19.56         8.35         8.52        28.08 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       19.96        54.81        35.05        20.84        15.58        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG 
       18.64        22.62        19.59        14.60        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       69.50        10.03        46.52        45.57        32.42        23.97 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       65.49        32.15        53.59        36.13        11.51        59.18 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        40.87        16.64         4.73        33.37        40.14 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       56.35        55.50        50.14        50.47        43.40        48.39 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UM 
       28.50        29.95        27.12        46.92         1.71        27.25 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
        4.34        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         0.16         3.91 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.36              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           155.77            210.67 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           27.795            21.275 
[1] "0.4 - 155.8 (27.8)" "0.0 - 210.7 (21.3)"
[1] "hr=" "1.4"
D11V2, continuous
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED    22  12   4   1
  6P GAIN WILD-TYPE 113  58  17   7
D11V3, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              22               113
  T2              12                58
  T3               4                17
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    24   6
  6P GAIN WILD-TYPE 105  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     24    6
  6P GAIN WILD-TYPE  105   50
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              24               105
  1               6                50
[1] 2 2
[1] FALSE
D11V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   18  2
  6P GAIN WILD-TYPE 90  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     18    2
  6P GAIN WILD-TYPE   90    8
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              18                90
  1               2                 8
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    11  21
  6P GAIN WILD-TYPE  44 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     11   21
  6P GAIN WILD-TYPE   44  102
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               11                44
  YES              21               102
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED               0                               42
  6P GAIN WILD-TYPE             6                              200
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6P GAIN MUTATED                                               1
  6P GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6P GAIN MUTATED                                     4
  6P GAIN WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6P GAIN MUTATED                                           0
  6P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6P GAIN MUTATED                                              5
  6P GAIN WILD-TYPE                                           12
D11V7, multiclass
                                               clus
vv                                              6P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           42
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                5
                                               clus
vv                                              6P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            200
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, continuous
D11V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  1     5
  6P GAIN WILD-TYPE                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED                           5
  6P GAIN WILD-TYPE                        23
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           0    38
  6P GAIN WILD-TYPE                                         2   164
D11V10, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   5                14
  BLACK OR AFRICAN AMERICAN                               5                23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  38               164
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5  29
  6P GAIN WILD-TYPE  18 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5   29
  6P GAIN WILD-TYPE   18  133
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                18
  NOT HISPANIC OR LATINO              29               133
[1] 2 2
[1] FALSE
D11V12, continuous
D11V13, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    30  19
  6P GAIN WILD-TYPE 153  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     30   19
  6P GAIN WILD-TYPE  153   55
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  TUMOR FREE              30               153
  WITH TUMOR              19                55
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  6P GAIN MUTATED     0  23  24   1   3
  6P GAIN WILD-TYPE  18 106  91   0  21
D11V14, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  G1               0                18
  G2              23               106
  G3              24                91
  G4               1                 0
  GX               3                21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, continuous
D11V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6P GAIN MUTATED                                             5
  6P GAIN WILD-TYPE                                          33
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  6P GAIN MUTATED                                        3
  6P GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  6P GAIN MUTATED                                                 1
  6P GAIN WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6P GAIN MUTATED               11                  29
  6P GAIN WILD-TYPE             51                 114
D11V17, multiclass
                                                 clus
vv                                                6P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               11
  LIFELONG NON-SMOKER                                          29
                                                 clus
vv                                                6P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 51
  LIFELONG NON-SMOKER                                           114
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V18, continuous
D11V19, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    9  0
  6P GAIN WILD-TYPE 16  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9    0
  6P GAIN WILD-TYPE   16    3
                         clus
vv                        6P GAIN MUTATED 6P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  9                16
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D11V20, continuous
D11V21, continuous
D11V22, continuous
D11V23, continuous
D11V24, continuous
D11V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  6P GAIN MUTATED                                     0
  6P GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  6P GAIN MUTATED                                     0                       6
  6P GAIN WILD-TYPE                                   7                      30
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6P GAIN MUTATED                         0                       1
  6P GAIN WILD-TYPE                       1                       7
D11V26, multiclass
                                     clus
vv                                    6P GAIN MUTATED 6P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           6                30
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  6P GAIN MUTATED                                               0
  6P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  6P GAIN MUTATED                                                5
  6P GAIN WILD-TYPE                                             20
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6P GAIN MUTATED                                                                                  17
  6P GAIN WILD-TYPE                                                                                65
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6P GAIN MUTATED                                                                                             21
  6P GAIN WILD-TYPE                                                                                          100
D11V27, multiclass
                                                                                              clus
vv                                                                                             6P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              21
                                                                                              clus
vv                                                                                             6P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V28, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   14 10
  6P GAIN WILD-TYPE 57 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     14   10
  6P GAIN WILD-TYPE   57   64
         clus
vv        6P GAIN MUTATED 6P GAIN WILD-TYPE
  ABSENT               14                57
  PRESENT              10                64
[1] 2 2
[1] FALSE
D11V29, continuous
D11V30, continuous
D11V31, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    8 18
  6P GAIN WILD-TYPE 41 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      8   18
  6P GAIN WILD-TYPE   41   99
                                          clus
vv                                         6P GAIN MUTATED 6P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   8                41
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              18                99
[1] 2 2
[1] FALSE
D11V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6P GAIN MUTATED              0          11         17
  6P GAIN WILD-TYPE           15          43         68
D11V33, multiclass
              clus
vv             6P GAIN MUTATED 6P GAIN WILD-TYPE
  CURRENT USER               0                15
  FORMER USER               11                43
  NEVER USED                17                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V34, continuous
D11V35, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   12  4
  6P GAIN WILD-TYPE 80 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     12    4
  6P GAIN WILD-TYPE   80   14
         clus
vv        6P GAIN MUTATED 6P GAIN WILD-TYPE
  ABSENT               12                80
  PRESENT               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  6P GAIN MUTATED             0        18     1
  6P GAIN WILD-TYPE           5        82     1
D11V36, multiclass
             clus
vv            6P GAIN MUTATED 6P GAIN WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                18                82
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V37, continuous
D11V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  6P GAIN MUTATED         0        0         1         0        3        18
  6P GAIN WILD-TYPE       5        1         0         1       31        59
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  6P GAIN MUTATED           7        0         1          3          2
  6P GAIN WILD-TYPE        30        4         7          2          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  6P GAIN MUTATED           9         0          1          5         1
  6P GAIN WILD-TYPE        35         1          2         37         6
                   vv
clus                STAGE IVB
  6P GAIN MUTATED           0
  6P GAIN WILD-TYPE        12
D11V39, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                 3                31
  STAGE IB1               18                59
  STAGE IB2                7                30
  STAGE II                 0                 4
  STAGE IIA                1                 7
  STAGE IIA1               3                 2
  STAGE IIA2               2                 5
  STAGE IIB                9                35
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               5                37
  STAGE IVA                1                 6
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    21  15
  6Q GAIN WILD-TYPE 190  52
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               36               242 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               15                52 
$`6Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI 
       57.04        31.40        46.32        35.01        38.99        35.61 
TCGA-C5-A1ML TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-C5-A8XH 
       20.91        52.01        17.85       155.77         2.73        45.83 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A97N TCGA-EK-A2PM 
        8.28        39.55        31.73        26.01         0.36         0.59 
TCGA-EK-A2RA TCGA-HG-A2PA TCGA-IR-A3LH TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3Q8 
       40.96        25.41        78.71        28.37         8.28        44.61 
TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-UC-A7PD TCGA-VS-A8QH TCGA-VS-A952 
       11.38        17.23         2.96        11.67        39.78        58.45 
TCGA-VS-A953 TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UO 
       15.68        24.30        46.92        45.11        14.53        47.87 

$`6Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF 
        5.46        19.86        67.46        30.21        57.73        53.16 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        40.93         3.58        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        9.34        13.61        50.99         8.35       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        14.73         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       95.11        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76        55.63        69.96        95.67        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18        17.52        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        0.30        24.82         7.46        14.89        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       27.29        27.25        27.22        24.00        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
       60.72        26.27         6.64         1.51        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RD 
        0.43         0.36         1.45         0.13         4.31         0.10 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM 
        0.43        47.77         0.53         0.10         0.49         0.76 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92        15.22        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        8.32        15.55         1.22        23.84        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       31.36        36.26        20.98        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       28.31        14.01        35.44        10.55         1.12        17.75 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       16.57        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16        66.81       129.37        96.95        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU 
       15.58        18.15        21.11       209.59        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
        0.89        12.49         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y 
       19.56        17.82        19.56         8.35         8.52        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       34.62        19.96        54.81        35.05        20.84        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        69.50        10.03        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       32.42        23.97        19.96        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       36.13        11.51        59.18        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        33.37        40.14        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       51.32        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       27.12         1.71        27.25        47.47        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       15.85        14.53         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 
        5.16        18.25        17.75         4.34        16.24        15.42 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       26.01        29.26        67.59        19.13         0.69         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.36              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           155.77            210.67 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           31.565            21.275 
[1] "0.4 - 155.8 (31.6)" "0.0 - 210.7 (21.3)"
[1] "hr=" "1.9"
D12V2, continuous
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED    12   9   4   2
  6Q GAIN WILD-TYPE 123  61  17   6
D12V3, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              12               123
  T2               9                61
  T3               4                17
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    16   5
  6Q GAIN WILD-TYPE 113  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     16    5
  6Q GAIN WILD-TYPE  113   51
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              16               113
  1               5                51
[1] 2 2
[1] FALSE
D12V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   12  1
  6Q GAIN WILD-TYPE 96  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     12    1
  6Q GAIN WILD-TYPE   96    9
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              12                96
  1               1                 9
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7  16
  6Q GAIN WILD-TYPE  48 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7   16
  6Q GAIN WILD-TYPE   48  107
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                7                48
  YES              16               107
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED               0                               28
  6Q GAIN WILD-TYPE             6                              214
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6Q GAIN MUTATED                                               0
  6Q GAIN WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6Q GAIN MUTATED                                     3
  6Q GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6Q GAIN MUTATED                                           0
  6Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6Q GAIN MUTATED                                              5
  6Q GAIN WILD-TYPE                                           12
D12V7, multiclass
                                               clus
vv                                              6Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           28
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                5
                                               clus
vv                                              6Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            214
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, continuous
D12V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  1     2
  6Q GAIN WILD-TYPE                                7    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED                           4
  6Q GAIN WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           0    27
  6Q GAIN WILD-TYPE                                         2   175
D12V10, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               4                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  27               175
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     5  17
  6Q GAIN WILD-TYPE  18 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5   17
  6Q GAIN WILD-TYPE   18  145
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                18
  NOT HISPANIC OR LATINO              17               145
[1] 2 2
[1] FALSE
D12V12, continuous
D12V13, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    20  16
  6Q GAIN WILD-TYPE 163  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     20   16
  6Q GAIN WILD-TYPE  163   58
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  TUMOR FREE              20               163
  WITH TUMOR              16                58
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  6Q GAIN MUTATED     0  17  13   1   4
  6Q GAIN WILD-TYPE  18 112 102   0  20
D12V14, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  G1               0                18
  G2              17               112
  G3              13               102
  G4               1                 0
  GX               4                20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, continuous
D12V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6Q GAIN MUTATED                                             5
  6Q GAIN WILD-TYPE                                          33
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  6Q GAIN MUTATED                                        1
  6Q GAIN WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  6Q GAIN MUTATED                                                 1
  6Q GAIN WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6Q GAIN MUTATED                9                  18
  6Q GAIN WILD-TYPE             53                 125
D12V17, multiclass
                                                 clus
vv                                                6Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                9
  LIFELONG NON-SMOKER                                          18
                                                 clus
vv                                                6Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 53
  LIFELONG NON-SMOKER                                           125
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V18, continuous
D12V19, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    7  0
  6Q GAIN WILD-TYPE 18  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7    0
  6Q GAIN WILD-TYPE   18    3
                         clus
vv                        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  7                18
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D12V20, continuous
D12V21, continuous
D12V22, continuous
D12V23, continuous
D12V24, continuous
D12V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  6Q GAIN MUTATED                                     0
  6Q GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  6Q GAIN MUTATED                                     0                       5
  6Q GAIN WILD-TYPE                                   7                      31
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6Q GAIN MUTATED                         0                       1
  6Q GAIN WILD-TYPE                       1                       7
D12V26, multiclass
                                     clus
vv                                    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           5                31
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  6Q GAIN MUTATED                                               0
  6Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  6Q GAIN MUTATED                                                3
  6Q GAIN WILD-TYPE                                             22
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6Q GAIN MUTATED                                                                                  11
  6Q GAIN WILD-TYPE                                                                                71
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6Q GAIN MUTATED                                                                                             16
  6Q GAIN WILD-TYPE                                                                                          105
D12V27, multiclass
                                                                                              clus
vv                                                                                             6Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              16
                                                                                              clus
vv                                                                                             6Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           71
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V28, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    8  7
  6Q GAIN WILD-TYPE 63 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      8    7
  6Q GAIN WILD-TYPE   63   67
         clus
vv        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ABSENT                8                63
  PRESENT               7                67
[1] 2 2
[1] FALSE
D12V29, continuous
D12V30, continuous
D12V31, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     6  11
  6Q GAIN WILD-TYPE  43 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6   11
  6Q GAIN WILD-TYPE   43  106
                                          clus
vv                                         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              11               106
[1] 2 2
[1] FALSE
D12V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6Q GAIN MUTATED              0           7         14
  6Q GAIN WILD-TYPE           15          47         71
D12V33, multiclass
              clus
vv             6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CURRENT USER               0                15
  FORMER USER                7                47
  NEVER USED                14                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V34, continuous
D12V35, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    7  3
  6Q GAIN WILD-TYPE 85 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7    3
  6Q GAIN WILD-TYPE   85   15
         clus
vv        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ABSENT                7                85
  PRESENT               3                15
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  6Q GAIN MUTATED             0        15     1
  6Q GAIN WILD-TYPE           5        85     1
D12V36, multiclass
             clus
vv            6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                15                85
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V37, continuous
D12V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  6Q GAIN MUTATED         0        0         0         0        3        10
  6Q GAIN WILD-TYPE       5        1         1         1       31        67
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  6Q GAIN MUTATED           5        0         1          2          2
  6Q GAIN WILD-TYPE        32        4         7          3          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  6Q GAIN MUTATED           7         0          1          3         2
  6Q GAIN WILD-TYPE        37         1          2         39         5
                   vv
clus                STAGE IVB
  6Q GAIN MUTATED           0
  6Q GAIN WILD-TYPE        12
D12V39, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 3                31
  STAGE IB1               10                67
  STAGE IB2                5                32
  STAGE II                 0                 4
  STAGE IIA                1                 7
  STAGE IIA1               2                 3
  STAGE IIA2               2                 5
  STAGE IIB                7                37
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               3                39
  STAGE IVA                2                 5
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    23  12
  7P GAIN WILD-TYPE 188  55
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               35               243 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               12                55 
$`7P GAIN MUTATED`
TCGA-C5-A1BL TCGA-C5-A1MK TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A7CH 
      173.29         2.43        73.18        78.35       100.14       154.32 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A8YQ TCGA-DG-A2KJ 
      147.35        17.19       131.11        94.95        23.51        95.11 
TCGA-EA-A50E TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A40J 
        7.46        12.59         1.51        15.55        23.84        14.01 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A69B TCGA-MA-AA41 TCGA-MY-A913 TCGA-Q1-A6DT 
       36.36        21.44        28.37         8.35        17.23         9.04 
TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A8QF 
       19.59        12.16        23.97        19.96        11.51        59.18 
TCGA-VS-A953 TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9V4 
       15.68        29.95        24.30        46.92         4.34 

$`7P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM 
       68.84        18.74        36.56       144.16       177.04        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       35.01        57.73        53.16        38.99        35.61         0.46 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93         3.58        44.22        73.45        83.05 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UE 
      210.67       101.82       134.33        15.48        20.35       155.77 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
      146.86        99.91        27.52        20.81        20.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76        55.63        69.96        95.67        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        31.73        26.01         0.30        24.82 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        25.91        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       24.00        13.48         0.36        60.72        26.27         6.64 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       19.27         0.39         0.43         0.59         0.36         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL 
        0.13        40.96         4.31         0.10         0.43        47.77 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
        0.53         0.10         0.49         0.76         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92        15.22        14.70        19.79         8.32         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48        16.14        28.31        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       17.75        25.41        16.57        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        29.85        27.42         3.29        24.56 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       20.48        15.58         8.28        18.15        21.11       209.59 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
       44.61        20.91        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.82        13.35        22.52        19.56        17.82        19.56 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       35.05        20.84         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB 
       22.62        14.60        11.67        93.99        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       46.52        45.57        32.42        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       36.13        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       33.37        40.14        58.45        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UC 
       51.32        50.47        43.40        48.39        28.50        27.12 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       45.11         1.71        14.53        27.25        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       41.52        26.07        15.85        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 
       67.20        18.84         5.16        18.25        17.75        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.51              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           173.29            210.67 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            23.51             22.98 
[1] "1.5 - 173.3 (23.5)" "0.0 - 210.7 (23.0)"
[1] "hr=" "1.2"
D13V2, continuous
                   vv
clus                 T1  T2  T3  T4
  7P GAIN MUTATED     9   8   3   4
  7P GAIN WILD-TYPE 126  62  18   4
D13V3, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               9               126
  T2               8                62
  T3               3                18
  T4               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    12   5
  7P GAIN WILD-TYPE 117  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     12    5
  7P GAIN WILD-TYPE  117   51
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              12               117
  1               5                51
[1] 2 2
[1] FALSE
D13V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    9  3
  7P GAIN WILD-TYPE 99  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9    3
  7P GAIN WILD-TYPE   99    7
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0               9                99
  1               3                 7
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     5  21
  7P GAIN WILD-TYPE  50 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5   21
  7P GAIN WILD-TYPE   50  102
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                5                50
  YES              21               102
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED               0                               35
  7P GAIN WILD-TYPE             6                              207
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7P GAIN MUTATED                                               0
  7P GAIN WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7P GAIN MUTATED                                     2
  7P GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7P GAIN MUTATED                                           0
  7P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7P GAIN MUTATED                                              1
  7P GAIN WILD-TYPE                                           16
D13V7, multiclass
                                               clus
vv                                              7P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           35
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              7P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            207
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, continuous
D13V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     1
  7P GAIN WILD-TYPE                                7    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED                           5
  7P GAIN WILD-TYPE                        23
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           0    28
  7P GAIN WILD-TYPE                                         2   174
D13V10, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               5                23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  28               174
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     4  18
  7P GAIN WILD-TYPE  19 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4   18
  7P GAIN WILD-TYPE   19  144
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                19
  NOT HISPANIC OR LATINO              18               144
[1] 2 2
[1] FALSE
D13V12, continuous
D13V13, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    20  14
  7P GAIN WILD-TYPE 163  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     20   14
  7P GAIN WILD-TYPE  163   60
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  TUMOR FREE              20               163
  WITH TUMOR              14                60
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  7P GAIN MUTATED     1  15  17   0   5
  7P GAIN WILD-TYPE  17 114  98   1  19
D13V14, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  G1               1                17
  G2              15               114
  G3              17                98
  G4               0                 1
  GX               5                19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, continuous
D13V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7P GAIN MUTATED                                             3
  7P GAIN WILD-TYPE                                          35
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  7P GAIN MUTATED                                        1
  7P GAIN WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  7P GAIN MUTATED                                                 1
  7P GAIN WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7P GAIN MUTATED                8                  19
  7P GAIN WILD-TYPE             54                 124
D13V17, multiclass
                                                 clus
vv                                                7P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                8
  LIFELONG NON-SMOKER                                          19
                                                 clus
vv                                                7P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    35
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 54
  LIFELONG NON-SMOKER                                           124
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V18, continuous
D13V19, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    3  1
  7P GAIN WILD-TYPE 22  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3    1
  7P GAIN WILD-TYPE   22    2
                         clus
vv                        7P GAIN MUTATED 7P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  3                22
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D13V20, continuous
D13V21, continuous
D13V22, continuous
D13V23, continuous
D13V24, continuous
D13V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  7P GAIN MUTATED                                     0
  7P GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  7P GAIN MUTATED                                     0                       3
  7P GAIN WILD-TYPE                                   7                      33
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7P GAIN MUTATED                         1                       0
  7P GAIN WILD-TYPE                       0                       8
D13V26, multiclass
                                     clus
vv                                    7P GAIN MUTATED 7P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           3                33
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           0                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  7P GAIN MUTATED                                               0
  7P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  7P GAIN MUTATED                                                2
  7P GAIN WILD-TYPE                                             23
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7P GAIN MUTATED                                                                                  15
  7P GAIN WILD-TYPE                                                                                67
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7P GAIN MUTATED                                                                                             13
  7P GAIN WILD-TYPE                                                                                          108
D13V27, multiclass
                                                                                              clus
vv                                                                                             7P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              13
                                                                                              clus
vv                                                                                             7P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V28, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    3  9
  7P GAIN WILD-TYPE 68 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3    9
  7P GAIN WILD-TYPE   68   65
         clus
vv        7P GAIN MUTATED 7P GAIN WILD-TYPE
  ABSENT                3                68
  PRESENT               9                65
[1] 2 2
[1] FALSE
D13V29, continuous
D13V30, continuous
D13V31, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     6  14
  7P GAIN WILD-TYPE  43 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6   14
  7P GAIN WILD-TYPE   43  103
                                          clus
vv                                         7P GAIN MUTATED 7P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              14               103
[1] 2 2
[1] FALSE
D13V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7P GAIN MUTATED              1           4          8
  7P GAIN WILD-TYPE           14          50         77
D13V33, multiclass
              clus
vv             7P GAIN MUTATED 7P GAIN WILD-TYPE
  CURRENT USER               1                14
  FORMER USER                4                50
  NEVER USED                 8                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V34, continuous
D13V35, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    8  2
  7P GAIN WILD-TYPE 84 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8    2
  7P GAIN WILD-TYPE   84   16
         clus
vv        7P GAIN MUTATED 7P GAIN WILD-TYPE
  ABSENT                8                84
  PRESENT               2                16
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  7P GAIN MUTATED             1        19     0
  7P GAIN WILD-TYPE           4        81     2
D13V36, multiclass
             clus
vv            7P GAIN MUTATED 7P GAIN WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                19                81
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V37, continuous
[1] "Remove cluster labels:" "7P GAIN MUTATED"       
clus
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-MA-AA42        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-ZX-AA5X 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
D13V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  7P GAIN MUTATED         1        0         0         0        4         5
  7P GAIN WILD-TYPE       4        1         1         1       30        72
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  7P GAIN MUTATED           3        0         2          1          0
  7P GAIN WILD-TYPE        34        4         6          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  7P GAIN MUTATED           7         0          1          7         5
  7P GAIN WILD-TYPE        37         1          2         35         2
                   vv
clus                STAGE IVB
  7P GAIN MUTATED           1
  7P GAIN WILD-TYPE        11
D13V39, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 4                30
  STAGE IB1                5                72
  STAGE IB2                3                34
  STAGE II                 0                 4
  STAGE IIA                2                 6
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                7                37
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               7                35
  STAGE IVA                5                 2
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    24  10
  7Q GAIN WILD-TYPE 187  57
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               34               244 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               10                57 
$`7Q GAIN MUTATED`
TCGA-C5-A1BL TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ 
      173.29        53.16         2.43        73.18        78.35       100.14 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A8YQ TCGA-DG-A2KJ 
      147.35        17.19       131.11        94.95        23.51        95.11 
TCGA-DR-A0ZL TCGA-DS-A3LQ TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EX-A8YF TCGA-FU-A23L 
       87.75        22.98        12.59         1.51        15.55        23.84 
TCGA-FU-A3NI TCGA-IR-A3LL TCGA-JW-A5VK TCGA-JW-A69B TCGA-MA-AA41 TCGA-MY-A913 
       20.98        36.36        20.48        28.37         8.35        17.23 
TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A953 TCGA-VS-A9U5 
       12.16        23.97        19.96        59.18        15.68        50.47 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9V3 TCGA-VS-A9V4 
       24.30        46.92        17.75         4.34 

$`7Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM 
       68.84        18.74        36.56       144.16       177.04        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML 
       35.01        57.73        38.99        35.61         0.46        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 
       40.93         3.58        44.22        73.45        83.05        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UE 
      154.32       101.82       134.33        15.48        20.35       155.77 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
      146.86        99.91        27.52        20.81        20.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK 
        1.12        82.06        44.94        63.98        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       55.63        69.96        95.67        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       31.73        26.01         0.30        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
       13.48         0.36        60.72        26.27         6.64        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
       40.96         4.31         0.10         0.43        47.77         0.53 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.49         0.76         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG 
       15.22        14.70        19.79         8.32         1.22        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       16.11        31.36        36.26        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       28.31        14.01        35.44        10.55         1.12        17.75 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41        16.57        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        29.85        27.42         3.29        24.56        21.44 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       15.58         8.28        18.15        21.11       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       20.91        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 
       13.35        22.52        19.56        17.82        19.56         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       22.62        19.59        14.60        11.67        93.99        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 
       10.03        46.52        45.57        32.42        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       53.59        36.13        11.51        39.78        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 
       16.64         4.73        33.37        40.14        58.45        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       55.50        50.14        51.32        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       29.95        27.12        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       47.87        47.47        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.51              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           173.29            210.67 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           23.905            22.095 
[1] "1.5 - 173.3 (23.9)" "0.0 - 210.7 (22.1)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                 T1  T2  T3  T4
  7Q GAIN MUTATED    12   5   5   4
  7Q GAIN WILD-TYPE 123  65  16   4
D14V3, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              12               123
  T2               5                65
  T3               5                16
  T4               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    11   6
  7Q GAIN WILD-TYPE 118  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     11    6
  7Q GAIN WILD-TYPE  118   50
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              11               118
  1               6                50
[1] 2 2
[1] FALSE
D14V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   10  3
  7Q GAIN WILD-TYPE 98  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     10    3
  7Q GAIN WILD-TYPE   98    7
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              10                98
  1               3                 7
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     4  20
  7Q GAIN WILD-TYPE  51 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4   20
  7Q GAIN WILD-TYPE   51  103
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                4                51
  YES              20               103
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED               0                               35
  7Q GAIN WILD-TYPE             6                              207
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7Q GAIN MUTATED                                               0
  7Q GAIN WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7Q GAIN MUTATED                                     1
  7Q GAIN WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7Q GAIN MUTATED                                           0
  7Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7Q GAIN MUTATED                                              1
  7Q GAIN WILD-TYPE                                           16
D14V7, multiclass
                                               clus
vv                                              7Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           35
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              7Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            207
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, continuous
D14V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     1
  7Q GAIN WILD-TYPE                                8    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED                           6
  7Q GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           0    26
  7Q GAIN WILD-TYPE                                         2   176
D14V10, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               6                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  26               176
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     3  16
  7Q GAIN WILD-TYPE  20 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3   16
  7Q GAIN WILD-TYPE   20  146
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                20
  NOT HISPANIC OR LATINO              16               146
[1] 2 2
[1] FALSE
D14V12, continuous
D14V13, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    22  11
  7Q GAIN WILD-TYPE 161  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     22   11
  7Q GAIN WILD-TYPE  161   63
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  TUMOR FREE              22               161
  WITH TUMOR              11                63
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  7Q GAIN MUTATED     1  13  18   0   4
  7Q GAIN WILD-TYPE  17 116  97   1  20
D14V14, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  G1               1                17
  G2              13               116
  G3              18                97
  G4               0                 1
  GX               4                20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, continuous
D14V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7Q GAIN MUTATED                                             4
  7Q GAIN WILD-TYPE                                          34
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  7Q GAIN MUTATED                                        3
  7Q GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  7Q GAIN MUTATED                                                 1
  7Q GAIN WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7Q GAIN MUTATED                8                  15
  7Q GAIN WILD-TYPE             54                 128
D14V17, multiclass
                                                 clus
vv                                                7Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                8
  LIFELONG NON-SMOKER                                          15
                                                 clus
vv                                                7Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    34
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 54
  LIFELONG NON-SMOKER                                           128
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V18, continuous
D14V19, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5  1
  7Q GAIN WILD-TYPE 20  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5    1
  7Q GAIN WILD-TYPE   20    2
                         clus
vv                        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D14V20, continuous
D14V21, continuous
D14V22, continuous
D14V23, continuous
D14V24, continuous
D14V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  7Q GAIN MUTATED                                     0
  7Q GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  7Q GAIN MUTATED                                     0                       5
  7Q GAIN WILD-TYPE                                   7                      31
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7Q GAIN MUTATED                         0                       0
  7Q GAIN WILD-TYPE                       1                       8
D14V26, multiclass
                                     clus
vv                                    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           5                31
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  7Q GAIN MUTATED                                               0
  7Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  7Q GAIN MUTATED                                                1
  7Q GAIN WILD-TYPE                                             24
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7Q GAIN MUTATED                                                                                  13
  7Q GAIN WILD-TYPE                                                                                69
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7Q GAIN MUTATED                                                                                             14
  7Q GAIN WILD-TYPE                                                                                          107
D14V27, multiclass
                                                                                              clus
vv                                                                                             7Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              14
                                                                                              clus
vv                                                                                             7Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           69
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V28, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  8
  7Q GAIN WILD-TYPE 67 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    8
  7Q GAIN WILD-TYPE   67   66
         clus
vv        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ABSENT                4                67
  PRESENT               8                66
[1] 2 2
[1] FALSE
D14V29, continuous
D14V30, continuous
D14V31, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     6  14
  7Q GAIN WILD-TYPE  43 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6   14
  7Q GAIN WILD-TYPE   43  103
                                          clus
vv                                         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              14               103
[1] 2 2
[1] FALSE
D14V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7Q GAIN MUTATED              1           6          9
  7Q GAIN WILD-TYPE           14          48         76
D14V33, multiclass
              clus
vv             7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CURRENT USER               1                14
  FORMER USER                6                48
  NEVER USED                 9                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V34, continuous
D14V35, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7  1
  7Q GAIN WILD-TYPE 85 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7    1
  7Q GAIN WILD-TYPE   85   17
         clus
vv        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ABSENT                7                85
  PRESENT               1                17
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  7Q GAIN MUTATED             1        19     0
  7Q GAIN WILD-TYPE           4        81     2
D14V36, multiclass
             clus
vv            7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                19                81
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V37, continuous
[1] "Remove cluster labels:" "7Q GAIN MUTATED"       
clus
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-MA-AA42        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-ZX-AA5X 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
D14V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  7Q GAIN MUTATED         0        0         0         0        4         6
  7Q GAIN WILD-TYPE       5        1         1         1       30        71
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  7Q GAIN MUTATED           5        0         1          1          0
  7Q GAIN WILD-TYPE        32        4         7          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  7Q GAIN MUTATED           5         0          1          8         3
  7Q GAIN WILD-TYPE        39         1          2         34         4
                   vv
clus                STAGE IVB
  7Q GAIN MUTATED           2
  7Q GAIN WILD-TYPE        10
D14V39, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 4                30
  STAGE IB1                6                71
  STAGE IB2                5                32
  STAGE II                 0                 4
  STAGE IIA                1                 7
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                5                39
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               8                34
  STAGE IVA                3                 4
  STAGE IVB                2                10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    39   9
  8P GAIN WILD-TYPE 172  58
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               48               230 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9                58 
$`8P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MH 
       57.04        82.85        19.86        67.46        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MP TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UH 
       35.61         3.58        18.02       210.67       154.32       131.11 
TCGA-C5-A8XI TCGA-C5-A8ZZ TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3Y4 TCGA-EA-A411 
        8.35        20.91        22.98        37.35        36.89        24.56 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A97N TCGA-EK-A2PM TCGA-EK-A2RN 
       24.82         7.46        25.91         0.36         0.59         0.53 
TCGA-EX-A8YF TCGA-FU-A3YQ TCGA-FU-A57G TCGA-IR-A3LL TCGA-JX-A3Q8 TCGA-MA-AA3X 
       15.55        28.31        35.44        36.36        44.61        19.56 
TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DW 
        8.35        11.38        20.84        17.23        16.41        17.56 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EJ TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A958 
       12.16        10.03        19.96        40.14        56.35        50.14 
TCGA-VS-A9UB TCGA-VS-A9UU TCGA-VS-A9V3 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXA 
       29.95        14.53        17.75        26.01        29.26         1.41 

$`8P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN 
       18.74        36.56       144.16       177.04       173.29         5.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MJ 
       31.40        46.32        30.21        35.01        57.73         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        2.43        20.91        40.93        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       17.85        20.42       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        17.19       155.77        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
        2.73        50.99        45.83       146.86        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       27.52        20.81        14.73         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       69.96        95.67        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        40.87        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 
       25.02        26.40        31.73        26.01         0.30        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       26.79        27.29        27.25        27.22        24.00        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        60.72        26.27         6.64         1.51        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.39         0.43         0.36         1.45         0.13        40.96 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK 
        4.31         0.10         0.43        47.77         0.10         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.76         0.03        20.35         7.92        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79         8.32         1.22        23.84        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       31.36        36.26        20.98        26.14         1.48        16.14 
TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       14.01        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       129.37        96.95        78.71        81.96        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       28.37         8.28        18.15        21.11       209.59        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI 
       22.52        17.82        19.56         8.52        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       19.96        54.81        35.05         2.96        15.58        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
        9.04        16.14        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       22.62        19.59        14.60        11.67        93.99        69.50 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 
       46.52        45.57        32.42        23.97        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       53.59        36.13        11.51        59.18        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 
       40.87        16.64         4.73        33.37        58.45        15.68 
TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       55.50        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       27.12        24.30        46.92        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
        4.34        16.24        15.42        67.59        19.13         0.69 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.36              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           210.67            209.59 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           23.770            23.065 
[1] "0.4 - 210.7 (23.8)" "0.0 - 209.6 (23.1)"
[1] "hr=" "1.3"
D15V2, continuous
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED    21  11   9   2
  8P GAIN WILD-TYPE 114  59  12   6
D15V3, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              21               114
  T2              11                59
  T3               9                12
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    23  12
  8P GAIN WILD-TYPE 106  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     23   12
  8P GAIN WILD-TYPE  106   44
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              23               106
  1              12                44
[1] 2 2
[1] FALSE
D15V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   19  4
  8P GAIN WILD-TYPE 89  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     19    4
  8P GAIN WILD-TYPE   89    6
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              19                89
  1               4                 6
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5 29
  8P GAIN WILD-TYPE 50 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5   29
  8P GAIN WILD-TYPE   50   94
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                5                50
  YES              29                94
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED               0                               50
  8P GAIN WILD-TYPE             6                              192
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8P GAIN MUTATED                                               0
  8P GAIN WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8P GAIN MUTATED                                     3
  8P GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8P GAIN MUTATED                                           0
  8P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8P GAIN MUTATED                                              0
  8P GAIN WILD-TYPE                                           17
D15V7, multiclass
                                               clus
vv                                              8P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              8P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            192
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, continuous
D15V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     2
  8P GAIN WILD-TYPE                                8    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED                           6
  8P GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           0    37
  8P GAIN WILD-TYPE                                         2   165
D15V10, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               6                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  37               165
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     4  30
  8P GAIN WILD-TYPE  19 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4   30
  8P GAIN WILD-TYPE   19  132
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                19
  NOT HISPANIC OR LATINO              30               132
[1] 2 2
[1] FALSE
D15V12, continuous
D15V13, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    32  12
  8P GAIN WILD-TYPE 151  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     32   12
  8P GAIN WILD-TYPE  151   62
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  TUMOR FREE              32               151
  WITH TUMOR              12                62
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  8P GAIN MUTATED     4  25  20   0   2
  8P GAIN WILD-TYPE  14 104  95   1  22
D15V14, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  G1               4                14
  G2              25               104
  G3              20                95
  G4               0                 1
  GX               2                22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, continuous
D15V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8P GAIN MUTATED                                             7
  8P GAIN WILD-TYPE                                          31
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  8P GAIN MUTATED                                        3
  8P GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  8P GAIN MUTATED                                                 2
  8P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8P GAIN MUTATED               11                  25
  8P GAIN WILD-TYPE             51                 118
D15V17, multiclass
                                                 clus
vv                                                8P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               2
  CURRENT SMOKER                                               11
  LIFELONG NON-SMOKER                                          25
                                                 clus
vv                                                8P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 51
  LIFELONG NON-SMOKER                                           118
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V18, continuous
D15V19, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  0
  8P GAIN WILD-TYPE 20  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    0
  8P GAIN WILD-TYPE   20    3
                         clus
vv                        8P GAIN MUTATED 8P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D15V20, continuous
D15V21, continuous
D15V22, continuous
D15V23, continuous
D15V24, continuous
D15V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  8P GAIN MUTATED                                     0
  8P GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  8P GAIN MUTATED                                     1                       9
  8P GAIN WILD-TYPE                                   6                      27
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8P GAIN MUTATED                         1                       1
  8P GAIN WILD-TYPE                       0                       7
D15V26, multiclass
                                     clus
vv                                    8P GAIN MUTATED 8P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 6
  OTHER LOCATION, SPECIFY                           9                27
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  8P GAIN MUTATED                                               1
  8P GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  8P GAIN MUTATED                                                2
  8P GAIN WILD-TYPE                                             23
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8P GAIN MUTATED                                                                                  15
  8P GAIN WILD-TYPE                                                                                67
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8P GAIN MUTATED                                                                                             24
  8P GAIN WILD-TYPE                                                                                           97
D15V27, multiclass
                                                                                              clus
vv                                                                                             8P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              24
                                                                                              clus
vv                                                                                             8P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V28, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   10 14
  8P GAIN WILD-TYPE 61 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     10   14
  8P GAIN WILD-TYPE   61   60
         clus
vv        8P GAIN MUTATED 8P GAIN WILD-TYPE
  ABSENT               10                61
  PRESENT              14                60
[1] 2 2
[1] FALSE
D15V29, continuous
D15V30, continuous
D15V31, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   10 26
  8P GAIN WILD-TYPE 39 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     10   26
  8P GAIN WILD-TYPE   39   91
                                          clus
vv                                         8P GAIN MUTATED 8P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  10                39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              26                91
[1] 2 2
[1] FALSE
D15V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8P GAIN MUTATED              1          13         11
  8P GAIN WILD-TYPE           14          41         74
D15V33, multiclass
              clus
vv             8P GAIN MUTATED 8P GAIN WILD-TYPE
  CURRENT USER               1                14
  FORMER USER               13                41
  NEVER USED                11                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V34, continuous
D15V35, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   14  2
  8P GAIN WILD-TYPE 78 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     14    2
  8P GAIN WILD-TYPE   78   16
         clus
vv        8P GAIN MUTATED 8P GAIN WILD-TYPE
  ABSENT               14                78
  PRESENT               2                16
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  8P GAIN MUTATED             1        20     0
  8P GAIN WILD-TYPE           4        80     2
D15V36, multiclass
             clus
vv            8P GAIN MUTATED 8P GAIN WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                20                80
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V37, continuous
D15V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  8P GAIN MUTATED         1        0         0         0        5         9
  8P GAIN WILD-TYPE       4        1         1         1       29        68
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  8P GAIN MUTATED           9        1         1          0          1
  8P GAIN WILD-TYPE        28        3         7          5          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  8P GAIN MUTATED           9         0          1         11         1
  8P GAIN WILD-TYPE        35         1          2         31         6
                   vv
clus                STAGE IVB
  8P GAIN MUTATED           1
  8P GAIN WILD-TYPE        11
D15V39, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 5                29
  STAGE IB1                9                68
  STAGE IB2                9                28
  STAGE II                 1                 3
  STAGE IIA                1                 7
  STAGE IIA1               0                 5
  STAGE IIA2               1                 6
  STAGE IIB                9                35
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB              11                31
  STAGE IVA                1                 6
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    65  19
  8Q GAIN WILD-TYPE 146  48
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               84               194 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               19                48 
$`8Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MH 
       57.04        82.85        19.86        67.46        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MP TCGA-C5-A2LV TCGA-C5-A2LZ TCGA-C5-A3HE TCGA-C5-A7CG 
       35.61         3.58        73.45       100.14        18.02       210.67 
TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8ZZ 
      154.32       131.11        50.99         8.35        23.51        20.91 
TCGA-DG-A2KJ TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3Y4 TCGA-EA-A411 
       95.11        69.96        22.98        37.35        36.89        24.56 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A97N TCGA-EK-A2H0 
       24.82         7.46        14.89        25.91         0.36        60.72 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A3GN 
        6.64         1.51         0.59         0.43         0.53         0.03 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A57G 
        8.32        15.55        23.84        20.98        28.31        35.44 
TCGA-HG-A9SC TCGA-IR-A3LL TCGA-JW-A852 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AX 
       16.57        36.36         8.28        44.61        11.28        12.49 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A5YI 
       19.56        17.82         8.35         8.52        11.38        34.62 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73S 
       20.84        17.23        16.41         9.04        17.56        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EH 
       19.59        14.60        12.16        10.03        46.52        32.42 
TCGA-VS-A8EJ TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U6 
       19.96        40.14        15.68        56.35        50.14        43.40 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V2 
       29.95        27.12        14.53         3.42        18.25        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       17.75         4.34        26.01        29.26        67.59         1.41 

$`8Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN 
       18.74        36.56       144.16       177.04       173.29         5.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MJ 
       31.40        46.32        30.21        35.01        57.73         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX 
        2.43        20.91        40.93        44.22        73.18        83.05 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35        38.43        33.24        52.01        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH 
      155.77        94.95         9.34        13.61         2.73        45.83 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH 
      146.86        99.91        27.52        20.81        14.73         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       55.63        95.67        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        40.87        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A5FO 
       25.02        26.40        31.73        26.01         0.30        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       27.29        27.25        27.22        24.00        13.48        12.59 
TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27        19.27         0.39         0.43         0.36         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A3GJ 
        0.13        40.96         4.31         0.10        47.77         0.10 
TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.49         0.76        20.35         7.92        15.22        14.70 
TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       19.79         1.22        19.04        16.11        31.36        36.26 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 
       26.14         1.48        16.14        14.01        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       17.75        25.41        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        29.85        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       20.48        15.58        28.37        18.15        21.11       209.59 
TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       20.91         0.89         0.30         0.82        13.35        22.52 
TCGA-MA-AA3Z TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA 
       19.56        28.08        19.96        54.81        35.05         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.58        15.95        16.14        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EI 
       18.64        11.67        93.99        69.50        45.57        23.97 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       65.49        32.15        53.59        36.13        11.51        59.18 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78        31.27        40.87        16.64         4.73        33.37 
TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UA 
       58.45        55.50        51.32        50.47        48.39        28.50 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       24.30        46.92        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UZ 
       47.87        47.47        41.52        26.07        15.85        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       18.84         5.16        16.24        15.42        19.13         0.69 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.03              0.10 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           210.67            209.59 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           20.875            24.430 
[1] "0.0 - 210.7 (20.9)" "0.1 - 209.6 (24.4)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED   38 17 12  6
  8Q GAIN WILD-TYPE 97 53  9  2
D16V3, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              38                97
  T2              17                53
  T3              12                 9
  T4               6                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   36 20
  8Q GAIN WILD-TYPE 93 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     36   20
  8Q GAIN WILD-TYPE   93   36
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              36                93
  1              20                36
[1] 2 2
[1] FALSE
D16V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   33  5
  8Q GAIN WILD-TYPE 75  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     33    5
  8Q GAIN WILD-TYPE   75    5
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              33                75
  1               5                 5
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   14 48
  8Q GAIN WILD-TYPE 41 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     14   48
  8Q GAIN WILD-TYPE   41   75
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               14                41
  YES              48                75
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED               2                               84
  8Q GAIN WILD-TYPE             4                              158
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8Q GAIN MUTATED                                               0
  8Q GAIN WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8Q GAIN MUTATED                                     3
  8Q GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8Q GAIN MUTATED                                           1
  8Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8Q GAIN MUTATED                                              1
  8Q GAIN WILD-TYPE                                           16
D16V7, multiclass
                                               clus
vv                                              8Q GAIN MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                           84
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              8Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            158
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, continuous
D16V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  1     4
  8Q GAIN WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED                           9
  8Q GAIN WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           0    62
  8Q GAIN WILD-TYPE                                         2   140
D16V10, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                               9                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  62               140
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     8  48
  8Q GAIN WILD-TYPE  15 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      8   48
  8Q GAIN WILD-TYPE   15  114
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                15
  NOT HISPANIC OR LATINO              48               114
[1] 2 2
[1] FALSE
D16V12, continuous
D16V13, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    53  24
  8Q GAIN WILD-TYPE 130  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     53   24
  8Q GAIN WILD-TYPE  130   50
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  TUMOR FREE              53               130
  WITH TUMOR              24                50
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  8Q GAIN MUTATED    5 38 37  0  8
  8Q GAIN WILD-TYPE 13 91 78  1 16
D16V14, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  G1               5                13
  G2              38                91
  G3              37                78
  G4               0                 1
  GX               8                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, continuous
D16V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8Q GAIN MUTATED                                            11
  8Q GAIN WILD-TYPE                                          27
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  8Q GAIN MUTATED                                        4
  8Q GAIN WILD-TYPE                                      5
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  8Q GAIN MUTATED                                                 2
  8Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8Q GAIN MUTATED               19                  41
  8Q GAIN WILD-TYPE             43                 102
D16V17, multiclass
                                                 clus
vv                                                8Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               2
  CURRENT SMOKER                                               19
  LIFELONG NON-SMOKER                                          41
                                                 clus
vv                                                8Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 43
  LIFELONG NON-SMOKER                                           102
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V18, continuous
D16V19, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    5  1
  8Q GAIN WILD-TYPE 20  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5    1
  8Q GAIN WILD-TYPE   20    2
                         clus
vv                        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D16V20, continuous
D16V21, continuous
D16V22, continuous
D16V23, continuous
D16V24, continuous
D16V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  8Q GAIN MUTATED                                     1
  8Q GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  8Q GAIN MUTATED                                     1                      12
  8Q GAIN WILD-TYPE                                   6                      24
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8Q GAIN MUTATED                         1                       1
  8Q GAIN WILD-TYPE                       0                       7
D16V26, multiclass
                                     clus
vv                                    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 6
  OTHER LOCATION, SPECIFY                          12                24
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  8Q GAIN MUTATED                                               1
  8Q GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  8Q GAIN MUTATED                                                8
  8Q GAIN WILD-TYPE                                             17
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8Q GAIN MUTATED                                                                                  30
  8Q GAIN WILD-TYPE                                                                                52
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8Q GAIN MUTATED                                                                                             35
  8Q GAIN WILD-TYPE                                                                                           86
D16V27, multiclass
                                                                                              clus
vv                                                                                             8Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              35
                                                                                              clus
vv                                                                                             8Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           52
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V28, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   15 20
  8Q GAIN WILD-TYPE 56 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     15   20
  8Q GAIN WILD-TYPE   56   54
         clus
vv        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ABSENT               15                56
  PRESENT              20                54
[1] 2 2
[1] FALSE
D16V29, continuous
D16V30, continuous
D16V31, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   14 44
  8Q GAIN WILD-TYPE 35 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     14   44
  8Q GAIN WILD-TYPE   35   73
                                          clus
vv                                         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  14                35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              44                73
[1] 2 2
[1] FALSE
D16V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8Q GAIN MUTATED              1          17         22
  8Q GAIN WILD-TYPE           14          37         63
D16V33, multiclass
              clus
vv             8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CURRENT USER               1                14
  FORMER USER               17                37
  NEVER USED                22                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V34, continuous
D16V35, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   21  4
  8Q GAIN WILD-TYPE 71 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     21    4
  8Q GAIN WILD-TYPE   71   14
         clus
vv        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ABSENT               21                71
  PRESENT               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  8Q GAIN MUTATED             1        36     0
  8Q GAIN WILD-TYPE           4        64     2
D16V36, multiclass
             clus
vv            8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                36                64
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V37, continuous
D16V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  8Q GAIN MUTATED         2        0         1         1        8        18
  8Q GAIN WILD-TYPE       3        1         0         0       26        59
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  8Q GAIN MUTATED          10        1         1          1          1
  8Q GAIN WILD-TYPE        27        3         7          4          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  8Q GAIN MUTATED          17         0          1         18         4
  8Q GAIN WILD-TYPE        27         1          2         24         3
                   vv
clus                STAGE IVB
  8Q GAIN MUTATED           3
  8Q GAIN WILD-TYPE         9
D16V39, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 0                 1
  STAGE IA1                1                 0
  STAGE IA2                1                 0
  STAGE IB                 8                26
  STAGE IB1               18                59
  STAGE IB2               10                27
  STAGE II                 1                 3
  STAGE IIA                1                 7
  STAGE IIA1               1                 4
  STAGE IIA2               1                 6
  STAGE IIB               17                27
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB              18                24
  STAGE IVA                4                 3
  STAGE IVB                3                 9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    35  10
  9P GAIN WILD-TYPE 176  57
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               45               233 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10                57 
$`9P GAIN MUTATED`
TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2M2 TCGA-C5-A7CG TCGA-C5-A7CK 
        3.58        73.18        73.45        33.24       210.67       134.33 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-DG-A2KL TCGA-DG-A2KM 
       15.48       147.35       155.77         2.73        44.94        63.98 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-EA-A5ZE TCGA-EK-A2H1 TCGA-EK-A2PK TCGA-EK-A2RN 
       22.98        16.83        27.25        26.27         0.39         0.53 
TCGA-EX-A3L1 TCGA-FU-A3TX TCGA-FU-A40J TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VL 
       15.22         1.48        14.01        36.36        27.42        15.58 
TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MY-A5BE 
       28.37        21.11        44.61        11.28         0.30        35.05 
TCGA-MY-A913 TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 
       17.23        11.67        12.16        32.42        65.49        32.15 
TCGA-VS-A8QC TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A9U5 TCGA-VS-A9UB 
       11.51        40.87        16.64        40.14        50.47        29.95 
TCGA-VS-A9UH TCGA-VS-A9UU TCGA-VS-A9V4 
       46.92        14.53         4.34 

$`9P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       30.21        35.01        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LX 
        0.46         2.43        20.91        40.93        44.22        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35       100.14        38.43        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH 
       20.42       154.32       101.82        20.35        17.19       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
       94.95         9.34        13.61        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
      146.86        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DR-A0ZM 
       14.73         1.12        95.11        82.06        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A7WF TCGA-DS-A7WH 
       36.76        55.63        69.96        95.67        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       31.73        26.01         0.30        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       26.79        25.91        27.29        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
        0.36        12.59        60.72         6.64         1.51        19.27 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.36         1.45         0.13        40.96 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK 
        4.31         0.10         0.43        47.77         0.10         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L 
        0.76         0.03        20.35         7.92        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        8.32        15.55         1.22        23.84        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36        36.26        20.98        26.14        16.14        28.31 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       35.44        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       129.37        96.95        78.71        81.96        29.85 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 TCGA-JW-AAVH 
        3.29        24.56        21.44        20.48         8.28        18.15 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU 
      209.59        20.91         0.89        12.49         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        19.56        17.82        19.56         8.35         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF 
       11.38        28.08        34.62        19.96        54.81        20.84 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59        14.60        93.99        69.50        10.03        46.52 
TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF 
       45.57        23.97        19.96        53.59        36.13        59.18 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 
       39.78        31.27         4.73        33.37        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 
       56.35        55.50        50.14        51.32        43.40        48.39 
TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       28.50        27.12        24.30        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
       17.75        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         1.41         0.16         3.91 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.30              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           210.67            209.59 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            27.25             22.52 
[1] "0.3 - 210.7 (27.2)" "0.0 - 209.6 (22.5)"
[1] "hr=" "1.2"
D17V2, continuous
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED    16  15   6   2
  9P GAIN WILD-TYPE 119  55  15   6
D17V3, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1              16               119
  T2              15                55
  T3               6                15
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    16  13
  9P GAIN WILD-TYPE 113  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     16   13
  9P GAIN WILD-TYPE  113   43
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              16               113
  1              13                43
[1] 2 2
[1] FALSE
D17V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   16  1
  9P GAIN WILD-TYPE 92  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     16    1
  9P GAIN WILD-TYPE   92    9
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              16                92
  1               1                 9
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    9 25
  9P GAIN WILD-TYPE 46 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      9   25
  9P GAIN WILD-TYPE   46   98
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                9                46
  YES              25                98
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED               0                               42
  9P GAIN WILD-TYPE             6                              200
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9P GAIN MUTATED                                               1
  9P GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9P GAIN MUTATED                                     4
  9P GAIN WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9P GAIN MUTATED                                           0
  9P GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9P GAIN MUTATED                                              2
  9P GAIN WILD-TYPE                                           15
D17V7, multiclass
                                               clus
vv                                              9P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           42
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              9P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            200
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, continuous
D17V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  3     4
  9P GAIN WILD-TYPE                                5    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED                           7
  9P GAIN WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           0    24
  9P GAIN WILD-TYPE                                         2   178
D17V10, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 5
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                               7                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  24               178
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     4  17
  9P GAIN WILD-TYPE  19 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4   17
  9P GAIN WILD-TYPE   19  145
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                19
  NOT HISPANIC OR LATINO              17               145
[1] 2 2
[1] FALSE
D17V12, continuous
D17V13, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    32   9
  9P GAIN WILD-TYPE 151  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     32    9
  9P GAIN WILD-TYPE  151   65
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  TUMOR FREE              32               151
  WITH TUMOR               9                65
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  9P GAIN MUTATED     4  20  20   0   2
  9P GAIN WILD-TYPE  14 109  95   1  22
D17V14, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  G1               4                14
  G2              20               109
  G3              20                95
  G4               0                 1
  GX               2                22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, continuous
D17V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9P GAIN MUTATED                                             4
  9P GAIN WILD-TYPE                                          34
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  9P GAIN MUTATED                                        2
  9P GAIN WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  9P GAIN MUTATED                                                 2
  9P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9P GAIN MUTATED               12                  23
  9P GAIN WILD-TYPE             50                 120
D17V17, multiclass
                                                 clus
vv                                                9P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               2
  CURRENT SMOKER                                               12
  LIFELONG NON-SMOKER                                          23
                                                 clus
vv                                                9P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    34
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 50
  LIFELONG NON-SMOKER                                           120
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V18, continuous
D17V19, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    2  0
  9P GAIN WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    0
  9P GAIN WILD-TYPE   23    3
                         clus
vv                        9P GAIN MUTATED 9P GAIN WILD-TYPE
  COMPLETED AS PLANNED                  2                23
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D17V20, continuous
D17V21, continuous
D17V22, continuous
D17V23, continuous
D17V24, continuous
D17V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  9P GAIN MUTATED                                     0
  9P GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  9P GAIN MUTATED                                     0                       8
  9P GAIN WILD-TYPE                                   7                      28
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9P GAIN MUTATED                         0                       1
  9P GAIN WILD-TYPE                       1                       7
D17V26, multiclass
                                     clus
vv                                    9P GAIN MUTATED 9P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           8                28
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  9P GAIN MUTATED                                               0
  9P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  9P GAIN MUTATED                                                4
  9P GAIN WILD-TYPE                                             21
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9P GAIN MUTATED                                                                                  10
  9P GAIN WILD-TYPE                                                                                72
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9P GAIN MUTATED                                                                                             22
  9P GAIN WILD-TYPE                                                                                           99
D17V27, multiclass
                                                                                              clus
vv                                                                                             9P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              22
                                                                                              clus
vv                                                                                             9P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           72
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V28, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   10 12
  9P GAIN WILD-TYPE 61 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     10   12
  9P GAIN WILD-TYPE   61   62
         clus
vv        9P GAIN MUTATED 9P GAIN WILD-TYPE
  ABSENT               10                61
  PRESENT              12                62
[1] 2 2
[1] FALSE
D17V29, continuous
D17V30, continuous
D17V31, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    11  12
  9P GAIN WILD-TYPE  38 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     11   12
  9P GAIN WILD-TYPE   38  105
                                          clus
vv                                         9P GAIN MUTATED 9P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  11                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              12               105
[1] 2 2
[1] FALSE
D17V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9P GAIN MUTATED              3           8         13
  9P GAIN WILD-TYPE           12          46         72
D17V33, multiclass
              clus
vv             9P GAIN MUTATED 9P GAIN WILD-TYPE
  CURRENT USER               3                12
  FORMER USER                8                46
  NEVER USED                13                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V34, continuous
D17V35, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   12  0
  9P GAIN WILD-TYPE 80 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     12    0
  9P GAIN WILD-TYPE   80   18
         clus
vv        9P GAIN MUTATED 9P GAIN WILD-TYPE
  ABSENT               12                80
  PRESENT               0                18
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  9P GAIN MUTATED             0        25     1
  9P GAIN WILD-TYPE           5        75     1
D17V36, multiclass
             clus
vv            9P GAIN MUTATED 9P GAIN WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                25                75
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V37, continuous
D17V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  9P GAIN MUTATED         0        0         0         0        6        10
  9P GAIN WILD-TYPE       5        1         1         1       28        67
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  9P GAIN MUTATED           7        0         3          1          0
  9P GAIN WILD-TYPE        30        4         5          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  9P GAIN MUTATED           7         0          1          9         4
  9P GAIN WILD-TYPE        37         1          2         33         3
                   vv
clus                STAGE IVB
  9P GAIN MUTATED           0
  9P GAIN WILD-TYPE        12
D17V39, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 6                28
  STAGE IB1               10                67
  STAGE IB2                7                30
  STAGE II                 0                 4
  STAGE IIA                3                 5
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                7                37
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               9                33
  STAGE IVA                4                 3
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    32  10
  9Q GAIN WILD-TYPE 179  57
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               42               236 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               10                57 
$`9Q GAIN MUTATED`
TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CG TCGA-C5-A7CK TCGA-C5-A7CL 
        3.58        73.18        73.45       210.67       134.33        15.48 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A8ZZ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A3LQ 
      147.35       155.77        20.91        44.94        63.98        22.98 
TCGA-EA-A5ZE TCGA-EK-A2H1 TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2RN TCGA-EX-A3L1 
       27.25        26.27         0.39         0.59         0.53        15.22 
TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VL 
        1.48        28.31        14.01        36.36        27.42        15.58 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MY-A5BE TCGA-MY-A913 TCGA-Q1-A6DT 
        8.28        11.28         0.30        35.05        17.23         9.04 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A94W 
       11.67        12.16        32.42        32.15        11.51        40.87 
TCGA-VS-A94X TCGA-VS-A9UB TCGA-VS-A9UH TCGA-VS-A9UU TCGA-VS-A9V4 TCGA-ZJ-AAXA 
       16.64        29.95        46.92        14.53         4.34         1.41 

$`9Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       30.21        35.01        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LX 
        0.46         2.43        20.91        40.93        44.22        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UC 
       17.85        20.42       154.32       101.82        20.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      131.11        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       45.83         8.35       146.86        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DR-A0ZL 
       20.81        14.73         1.12        95.11        82.06        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        36.76        55.63        69.96        95.67        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        31.73        26.01         0.30        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF 
        7.46        14.89        26.79        25.91        27.29        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       24.00        13.48         0.36        12.59        60.72         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        1.51        19.27         0.43         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ 
       40.96         4.31         0.10         0.43        47.77         0.10 
TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 
        0.49         0.76         0.03        20.35         7.92        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         8.32        15.55         1.22        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       16.11        31.36        36.26        20.98        26.14        16.14 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       35.44        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       129.37        96.95        78.71        81.96        29.85 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH 
        3.29        24.56        21.44        20.48        28.37        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        44.61        20.91         0.89        12.49 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.82        13.35        22.52        19.56        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        8.35         8.52        11.38        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       54.81        20.84         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB 
       22.62        19.59        14.60        93.99        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 
       46.52        45.57        23.97        19.96        65.49        53.59 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94Y TCGA-VS-A94Z 
       36.13        59.18        39.78        31.27         4.73        33.37 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       40.14        58.45        15.68        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UC 
       51.32        50.47        43.40        48.39        28.50        27.12 
TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       24.30        45.11         1.71        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY 
       47.47        41.52        26.07        15.85         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 
       67.20        18.84         5.16        18.25        17.75        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.30              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           210.67            209.59 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           19.070            23.755 
[1] "0.3 - 210.7 (19.1)" "0.0 - 209.6 (23.8)"
[1] "hr=" "1"  
D18V2, continuous
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED    15  13   5   2
  9Q GAIN WILD-TYPE 120  57  16   6
D18V3, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              15               120
  T2              13                57
  T3               5                16
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    16  13
  9Q GAIN WILD-TYPE 113  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     16   13
  9Q GAIN WILD-TYPE  113   43
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              16               113
  1              13                43
[1] 2 2
[1] FALSE
D18V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   14  1
  9Q GAIN WILD-TYPE 94  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     14    1
  9Q GAIN WILD-TYPE   94    9
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              14                94
  1               1                 9
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     9  21
  9Q GAIN WILD-TYPE  46 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      9   21
  9Q GAIN WILD-TYPE   46  102
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                9                46
  YES              21               102
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED               0                               44
  9Q GAIN WILD-TYPE             6                              198
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9Q GAIN MUTATED                                               1
  9Q GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9Q GAIN MUTATED                                     1
  9Q GAIN WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9Q GAIN MUTATED                                           0
  9Q GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9Q GAIN MUTATED                                              1
  9Q GAIN WILD-TYPE                                           16
D18V7, multiclass
                                               clus
vv                                              9Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           44
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              9Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            198
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, continuous
D18V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  3     4
  9Q GAIN WILD-TYPE                                5    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED                           6
  9Q GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           0    24
  9Q GAIN WILD-TYPE                                         2   178
D18V10, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 5
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                               6                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  24               178
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     4  18
  9Q GAIN WILD-TYPE  19 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4   18
  9Q GAIN WILD-TYPE   19  144
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                19
  NOT HISPANIC OR LATINO              18               144
[1] 2 2
[1] FALSE
D18V12, continuous
D18V13, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    29  10
  9Q GAIN WILD-TYPE 154  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     29   10
  9Q GAIN WILD-TYPE  154   64
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  TUMOR FREE              29               154
  WITH TUMOR              10                64
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  9Q GAIN MUTATED     5  20  17   0   2
  9Q GAIN WILD-TYPE  13 109  98   1  22
D18V14, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  G1               5                13
  G2              20               109
  G3              17                98
  G4               0                 1
  GX               2                22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, continuous
D18V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9Q GAIN MUTATED                                             3
  9Q GAIN WILD-TYPE                                          35
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  9Q GAIN MUTATED                                        3
  9Q GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  9Q GAIN MUTATED                                                 2
  9Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9Q GAIN MUTATED               12                  20
  9Q GAIN WILD-TYPE             50                 123
D18V17, multiclass
                                                 clus
vv                                                9Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               2
  CURRENT SMOKER                                               12
  LIFELONG NON-SMOKER                                          20
                                                 clus
vv                                                9Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    35
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 50
  LIFELONG NON-SMOKER                                           123
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V18, continuous
D18V19, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    2  0
  9Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    0
  9Q GAIN WILD-TYPE   23    3
                         clus
vv                        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                  2                23
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D18V20, continuous
D18V21, continuous
D18V22, continuous
D18V23, continuous
D18V24, continuous
D18V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  9Q GAIN MUTATED                                     0
  9Q GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  9Q GAIN MUTATED                                     0                       7
  9Q GAIN WILD-TYPE                                   7                      29
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9Q GAIN MUTATED                         0                       1
  9Q GAIN WILD-TYPE                       1                       7
D18V26, multiclass
                                     clus
vv                                    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           7                29
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  9Q GAIN MUTATED                                               0
  9Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  9Q GAIN MUTATED                                                3
  9Q GAIN WILD-TYPE                                             22
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9Q GAIN MUTATED                                                                                  10
  9Q GAIN WILD-TYPE                                                                                72
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9Q GAIN MUTATED                                                                                             20
  9Q GAIN WILD-TYPE                                                                                          101
D18V27, multiclass
                                                                                              clus
vv                                                                                             9Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              20
                                                                                              clus
vv                                                                                             9Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           72
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V28, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    9  9
  9Q GAIN WILD-TYPE 62 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      9    9
  9Q GAIN WILD-TYPE   62   65
         clus
vv        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ABSENT                9                62
  PRESENT               9                65
[1] 2 2
[1] FALSE
D18V29, continuous
D18V30, continuous
D18V31, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    11  16
  9Q GAIN WILD-TYPE  38 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11   16
  9Q GAIN WILD-TYPE   38  101
                                          clus
vv                                         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  11                38
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              16               101
[1] 2 2
[1] FALSE
D18V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9Q GAIN MUTATED              3           6          9
  9Q GAIN WILD-TYPE           12          48         76
D18V33, multiclass
              clus
vv             9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CURRENT USER               3                12
  FORMER USER                6                48
  NEVER USED                 9                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V34, continuous
D18V35, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    9  0
  9Q GAIN WILD-TYPE 83 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      9    0
  9Q GAIN WILD-TYPE   83   18
         clus
vv        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ABSENT                9                83
  PRESENT               0                18
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  9Q GAIN MUTATED             0        21     1
  9Q GAIN WILD-TYPE           5        79     1
D18V36, multiclass
             clus
vv            9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                21                79
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V37, continuous
D18V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  9Q GAIN MUTATED         1        0         0         0        6         9
  9Q GAIN WILD-TYPE       4        1         1         1       28        68
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  9Q GAIN MUTATED           5        0         3          1          0
  9Q GAIN WILD-TYPE        32        4         5          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  9Q GAIN MUTATED           8         0          0          9         4
  9Q GAIN WILD-TYPE        36         1          3         33         3
                   vv
clus                STAGE IVB
  9Q GAIN MUTATED           0
  9Q GAIN WILD-TYPE        12
D18V39, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 6                28
  STAGE IB1                9                68
  STAGE IB2                5                32
  STAGE II                 0                 4
  STAGE IIA                3                 5
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                8                36
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               9                33
  STAGE IVA                4                 3
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    15   8
  10P GAIN WILD-TYPE 196  59
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                23                255 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                 59 
$`10P GAIN MUTATED`
TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A7X5 
      173.29        35.01        57.73       100.14       154.32        13.61 
TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-DG-A2KH TCGA-DS-A0VK TCGA-EA-A97N TCGA-EK-A2PG 
       45.83        23.51         1.12        36.76         0.36         1.51 
TCGA-FU-A3NI TCGA-GH-A9DA TCGA-HM-A4S6 TCGA-IR-A3LL TCGA-LP-A4AW TCGA-MA-AA3W 
       20.98        17.75        14.93        36.36         0.89        22.52 
TCGA-MA-AA41 TCGA-VS-A8EI TCGA-VS-A9U5 TCGA-VS-A9UL TCGA-XS-A8TJ 
        8.35        23.97        50.47        14.53        29.26 

$`10P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM 
       68.84        18.74        36.56       144.16       177.04        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       40.93         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       210.67       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      147.35        17.19       155.77       131.11        94.95         9.34 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR 
        2.73        50.99         8.35       146.86        99.91        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.81        20.91        14.73        95.11        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       63.98        87.75        58.88        55.63        69.96        95.67 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       40.87        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        36.89        26.40        24.56        31.73        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        0.30        24.82         7.46        14.89        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       27.29        27.25        27.22        24.00        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL 
       60.72        26.27         6.64        19.27         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC 
        0.59         0.36         1.45         0.13        40.96         4.31 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.10         0.43        47.77         0.53         0.10         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.76         0.03        20.35         7.92        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         8.32        15.55         1.22        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       16.11        31.36        36.26        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
       28.31        14.01        35.44        10.55         1.12        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       16.57        21.67        20.78         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       129.37        96.95        78.71        81.96        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       20.91        11.28        12.49         0.30         0.82        13.35 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       19.56        17.82        19.56         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       34.62        19.96        54.81        35.05        20.84        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59        14.60        11.67        93.99        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        46.52        45.57        32.42        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        53.59        36.13        11.51        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        40.87        16.64         4.73        33.37        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       58.45        15.68        56.35        55.50        50.14        51.32 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       43.40        48.39        28.50        29.95        27.12        24.30 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       46.92        45.11         1.71        27.25        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       41.52        26.07        15.85        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       67.20        18.84         5.16        18.25        17.75         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       16.24        15.42        26.01        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.36               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            173.29             210.67 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             23.51              22.98 
[1] "0.4 - 173.3 (23.5)" "0.0 - 210.7 (23.0)"
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED    13   2   4   0
  10P GAIN WILD-TYPE 122  68  17   8
D19V3, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               13                122
  T2                2                 68
  T3                4                 17
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     8   8
  10P GAIN WILD-TYPE 121  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8    8
  10P GAIN WILD-TYPE  121   48
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                8                121
  1                8                 48
[1] 2 2
[1] FALSE
D19V5, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   11  1
  10P GAIN WILD-TYPE 97  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     11    1
  10P GAIN WILD-TYPE   97    9
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               11                 97
  1                1                  9
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     4  12
  10P GAIN WILD-TYPE  51 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4   12
  10P GAIN WILD-TYPE   51  111
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 4                 51
  YES               12                111
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED               1                               22
  10P GAIN WILD-TYPE             5                              220
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10P GAIN MUTATED                                               0
  10P GAIN WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10P GAIN MUTATED                                     2
  10P GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10P GAIN MUTATED                                           0
  10P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10P GAIN MUTATED                                              0
  10P GAIN WILD-TYPE                                           17
D19V7, multiclass
                                               clus
vv                                              10P GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            22
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              10P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             220
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, continuous
D19V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     1
  10P GAIN WILD-TYPE                                8    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED                           3
  10P GAIN WILD-TYPE                        25
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           0    19
  10P GAIN WILD-TYPE                                         2   183
D19V10, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                3                 25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   19                183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3  15
  10P GAIN WILD-TYPE  20 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3   15
  10P GAIN WILD-TYPE   20  147
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 20
  NOT HISPANIC OR LATINO               15                147
[1] 2 2
[1] FALSE
D19V12, continuous
D19V13, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    14   7
  10P GAIN WILD-TYPE 169  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     14    7
  10P GAIN WILD-TYPE  169   67
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  TUMOR FREE               14                169
  WITH TUMOR                7                 67
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  10P GAIN MUTATED     2   9  10   0   2
  10P GAIN WILD-TYPE  16 120 105   1  22
D19V14, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  G1                2                 16
  G2                9                120
  G3               10                105
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, continuous
D19V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10P GAIN MUTATED                                             5
  10P GAIN WILD-TYPE                                          33
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  10P GAIN MUTATED                                        1
  10P GAIN WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  10P GAIN MUTATED                                                 1
  10P GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10P GAIN MUTATED                6                   8
  10P GAIN WILD-TYPE             56                 135
D19V17, multiclass
                                                 clus
vv                                                10P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 6
  LIFELONG NON-SMOKER                                            8
                                                 clus
vv                                                10P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  56
  LIFELONG NON-SMOKER                                            135
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V18, continuous
D19V19, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  0
  10P GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    0
  10P GAIN WILD-TYPE   23    3
                         clus
vv                        10P GAIN MUTATED 10P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   2                 23
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D19V20, continuous
D19V21, continuous
D19V22, continuous
D19V23, continuous
D19V24, continuous
D19V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  10P GAIN MUTATED                                     0
  10P GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  10P GAIN MUTATED                                     0
  10P GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  10P GAIN MUTATED                         5                       0
  10P GAIN WILD-TYPE                      31                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10P GAIN MUTATED                         1
  10P GAIN WILD-TYPE                       7
D19V26, multiclass
                                     clus
vv                                    10P GAIN MUTATED 10P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            5                 31
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  10P GAIN MUTATED                                               0
  10P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  10P GAIN MUTATED                                                2
  10P GAIN WILD-TYPE                                             23
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10P GAIN MUTATED                                                                                   6
  10P GAIN WILD-TYPE                                                                                76
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10P GAIN MUTATED                                                                                             11
  10P GAIN WILD-TYPE                                                                                          110
D19V27, multiclass
                                                                                              clus
vv                                                                                             10P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               11
                                                                                              clus
vv                                                                                             10P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            76
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V28, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4  8
  10P GAIN WILD-TYPE 67 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    8
  10P GAIN WILD-TYPE   67   66
         clus
vv        10P GAIN MUTATED 10P GAIN WILD-TYPE
  ABSENT                 4                 67
  PRESENT                8                 66
[1] 2 2
[1] FALSE
D19V29, continuous
D19V30, continuous
D19V31, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     7   8
  10P GAIN WILD-TYPE  42 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7    8
  10P GAIN WILD-TYPE   42  109
                                          clus
vv                                         10P GAIN MUTATED 10P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    7                 42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                8                109
[1] 2 2
[1] FALSE
D19V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10P GAIN MUTATED              0           5          6
  10P GAIN WILD-TYPE           15          49         79
D19V33, multiclass
              clus
vv             10P GAIN MUTATED 10P GAIN WILD-TYPE
  CURRENT USER                0                 15
  FORMER USER                 5                 49
  NEVER USED                  6                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V34, continuous
D19V35, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   10  1
  10P GAIN WILD-TYPE 82 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     10    1
  10P GAIN WILD-TYPE   82   17
         clus
vv        10P GAIN MUTATED 10P GAIN WILD-TYPE
  ABSENT                10                 82
  PRESENT                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  10P GAIN MUTATED             1         6     0
  10P GAIN WILD-TYPE           4        94     2
D19V36, multiclass
             clus
vv            10P GAIN MUTATED 10P GAIN WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                  6                 94
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V37, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 15 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MA-AA3Z         TCGA-MA-AA42         TCGA-MU-A51Y 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-MY-A913         TCGA-ZX-AA5X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D19V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  10P GAIN MUTATED         0        1         0         0        2        10
  10P GAIN WILD-TYPE       5        0         1         1       32        67
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  10P GAIN MUTATED           2        0         0          0          0
  10P GAIN WILD-TYPE        35        4         8          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  10P GAIN MUTATED           4         0          0          4         0
  10P GAIN WILD-TYPE        40         1          3         38         7
                    vv
clus                 STAGE IVB
  10P GAIN MUTATED           1
  10P GAIN WILD-TYPE        11
D19V39, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  1                  0
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  2                 32
  STAGE IB1                10                 67
  STAGE IB2                 2                 35
  STAGE II                  0                  4
  STAGE IIA                 0                  8
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 4                 40
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB                4                 38
  STAGE IVA                 0                  7
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    12   4
  10Q GAIN WILD-TYPE 199  63
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                16                262 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 63 
$`10Q GAIN MUTATED`
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-C5-A8XH TCGA-C5-A8YQ 
       35.01        57.73       100.14       154.32        45.83        23.51 
TCGA-DG-A2KH TCGA-EA-A97N TCGA-EK-A2PG TCGA-IR-A3LL TCGA-LP-A4AU TCGA-MA-AA3W 
        1.12         0.36         1.51        36.36        11.28        22.52 
TCGA-MA-AA41 TCGA-VS-A8EI TCGA-XS-A8TJ TCGA-ZJ-AAXA 
        8.35        23.97        29.26         1.41 

$`10Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       30.21        53.16        38.99        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19       155.77       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
        9.34        13.61         2.73        50.99         8.35       146.86 
TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ 
       99.91        27.52        20.81        20.91        14.73        95.11 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       55.63        69.96        95.67        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       17.52         8.28        39.55        40.87        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       24.56        31.73        26.01         0.30        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        25.91        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       24.00        13.48        12.59        60.72        26.27         6.64 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       19.27         0.39         0.43         0.59         0.36         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL 
        0.13        40.96         4.31         0.10         0.43        47.77 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
        0.53         0.10         0.49         0.76         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        7.92        15.22        14.70        19.79         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       20.98        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       35.44        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       129.37        96.95        78.71        81.96        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       20.91         0.89        12.49         0.30         0.82        13.35 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       19.56        17.82        19.56         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       34.62        19.96        54.81        35.05        20.84        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59        14.60        11.67        93.99        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        46.52        45.57        32.42        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        53.59        36.13        11.51        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        40.87        16.64         4.73        33.37        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       58.45        15.68        56.35        55.50        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       50.47        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       24.30        46.92        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       47.87        47.47        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ 
       17.75         4.34        16.24        15.42        26.01        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         0.16         3.91 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.36               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            154.32             210.67 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             23.74              22.80 
[1] "0.4 - 154.3 (23.7)" "0.0 - 210.7 (22.8)"
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED     8   2   3   0
  10Q GAIN WILD-TYPE 127  68  18   8
D20V3, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                8                127
  T2                2                 68
  T3                3                 18
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     6   6
  10Q GAIN WILD-TYPE 123  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    6
  10Q GAIN WILD-TYPE  123   50
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                6                123
  1                6                 50
[1] 2 2
[1] FALSE
D20V5, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   10  1
  10Q GAIN WILD-TYPE 98  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     10    1
  10Q GAIN WILD-TYPE   98    9
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               10                 98
  1                1                  9
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2   9
  10Q GAIN WILD-TYPE  53 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    9
  10Q GAIN WILD-TYPE   53  114
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                 53
  YES                9                114
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED               1                               14
  10Q GAIN WILD-TYPE             5                              228
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10Q GAIN MUTATED                                               0
  10Q GAIN WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10Q GAIN MUTATED                                     2
  10Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10Q GAIN MUTATED                                           0
  10Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10Q GAIN MUTATED                                              0
  10Q GAIN WILD-TYPE                                           17
D20V7, multiclass
                                               clus
vv                                              10Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            14
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              10Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             228
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, continuous
D20V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     1
  10Q GAIN WILD-TYPE                                8    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED                           2
  10Q GAIN WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           0    12
  10Q GAIN WILD-TYPE                                         2   190
D20V10, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                2                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   12                190
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   9
  10Q GAIN WILD-TYPE  20 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    9
  10Q GAIN WILD-TYPE   20  153
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 20
  NOT HISPANIC OR LATINO                9                153
[1] 2 2
[1] FALSE
D20V12, continuous
D20V13, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     9   4
  10Q GAIN WILD-TYPE 174  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      9    4
  10Q GAIN WILD-TYPE  174   70
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  TUMOR FREE                9                174
  WITH TUMOR                4                 70
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  10Q GAIN MUTATED     1   8   4   0   2
  10Q GAIN WILD-TYPE  17 121 111   1  22
D20V14, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  G1                1                 17
  G2                8                121
  G3                4                111
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V15, continuous
D20V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10Q GAIN MUTATED                                             3
  10Q GAIN WILD-TYPE                                          35
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  10Q GAIN MUTATED                                        1
  10Q GAIN WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  10Q GAIN MUTATED                                                 1
  10Q GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10Q GAIN MUTATED                4                   6
  10Q GAIN WILD-TYPE             58                 137
D20V17, multiclass
                                                 clus
vv                                                10Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                            6
                                                 clus
vv                                                10Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     35
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  58
  LIFELONG NON-SMOKER                                            137
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V18, continuous
D20V19, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    1  0
  10Q GAIN WILD-TYPE 24  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    0
  10Q GAIN WILD-TYPE   24    3
                         clus
vv                        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   1                 24
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D20V20, continuous
D20V21, continuous
D20V22, continuous
D20V23, continuous
D20V24, continuous
D20V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  10Q GAIN MUTATED                                     0
  10Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  10Q GAIN MUTATED                                     0
  10Q GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  10Q GAIN MUTATED                         4                       0
  10Q GAIN WILD-TYPE                      32                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10Q GAIN MUTATED                         0
  10Q GAIN WILD-TYPE                       8
D20V26, multiclass
                                     clus
vv                                    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            4                 32
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  10Q GAIN MUTATED                                               0
  10Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  10Q GAIN MUTATED                                                0
  10Q GAIN WILD-TYPE                                             25
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10Q GAIN MUTATED                                                                                   5
  10Q GAIN WILD-TYPE                                                                                77
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10Q GAIN MUTATED                                                                                              8
  10Q GAIN WILD-TYPE                                                                                          113
D20V27, multiclass
                                                                                              clus
vv                                                                                             10Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                8
                                                                                              clus
vv                                                                                             10Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               25
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            77
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V28, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  3
  10Q GAIN WILD-TYPE 68 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    3
  10Q GAIN WILD-TYPE   68   71
         clus
vv        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ABSENT                 3                 68
  PRESENT                3                 71
[1] 2 2
[1] FALSE
D20V29, continuous
D20V30, continuous
D20V31, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   6
  10Q GAIN WILD-TYPE  46 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    6
  10Q GAIN WILD-TYPE   46  111
                                          clus
vv                                         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 46
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                6                111
[1] 2 2
[1] FALSE
D20V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10Q GAIN MUTATED              0           4          2
  10Q GAIN WILD-TYPE           15          50         83
D20V33, multiclass
              clus
vv             10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CURRENT USER                0                 15
  FORMER USER                 4                 50
  NEVER USED                  2                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V34, continuous
D20V35, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    6  1
  10Q GAIN WILD-TYPE 86 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    1
  10Q GAIN WILD-TYPE   86   17
         clus
vv        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ABSENT                 6                 86
  PRESENT                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  10Q GAIN MUTATED             0         6     0
  10Q GAIN WILD-TYPE           5        94     2
D20V36, multiclass
             clus
vv            10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                  6                 94
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V37, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A3JK         TCGA-JW-A852 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-MA-AA3Z         TCGA-MA-AA42 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-ZX-AA5X 
"10Q GAIN WILD-TYPE" 
D20V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  10Q GAIN MUTATED         0        0         0         0        0         9
  10Q GAIN WILD-TYPE       5        1         1         1       34        68
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  10Q GAIN MUTATED           1        0         0          0          0
  10Q GAIN WILD-TYPE        36        4         8          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  10Q GAIN MUTATED           3         0          0          3         0
  10Q GAIN WILD-TYPE        41         1          3         39         7
                    vv
clus                 STAGE IVB
  10Q GAIN MUTATED           0
  10Q GAIN WILD-TYPE        12
D20V39, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  0                 34
  STAGE IB1                 9                 68
  STAGE IB2                 1                 36
  STAGE II                  0                  4
  STAGE IIA                 0                  8
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 3                 41
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB                3                 39
  STAGE IVA                 0                  7
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     6   2
  11P GAIN WILD-TYPE 205  65
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                270 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 65 
$`11P GAIN MUTATED`
TCGA-C5-A1M9 TCGA-C5-A2LT TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-FU-A40J TCGA-MY-A913 
       35.01        73.18        26.27        19.27        14.01        17.23 
TCGA-VS-A8EC TCGA-VS-A8Q8 
       46.52        32.15 

$`11P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       30.21        57.73        53.16        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
        2.43        20.91        40.93         3.58        44.22        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      131.11        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       45.83         8.35       146.86        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       20.81        20.91        14.73         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       69.96        95.67        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       31.73        26.01         0.30        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48         0.36        12.59        60.72         6.64         1.51 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
       40.96         4.31         0.10         0.43        47.77         0.53 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.49         0.76         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       15.22        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
       26.14         1.48        16.14        28.31        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12        17.75        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        8.28        18.15        21.11       209.59        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        19.56        17.82        19.56         8.35         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       22.62        19.59        14.60        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       69.50        10.03        45.57        32.42        23.97        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       65.49        53.59        36.13        11.51        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        40.87        16.64         4.73        33.37        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       58.45        15.68        56.35        55.50        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       50.47        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       24.30        46.92        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       47.87        47.47        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       17.75         4.34        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         0.69         1.41         0.16         3.91 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             14.01               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             73.18             210.67 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             29.21              22.80 
[1] "14.0 - 73.2 (29.2)" "0.0 - 210.7 (22.8)"
[1] "hr=" "1"  
D21V2, continuous
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED     2   1   2   0
  11P GAIN WILD-TYPE 133  69  19   8
D21V3, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                2                133
  T2                1                 69
  T3                2                 19
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     3   2
  11P GAIN WILD-TYPE 126  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    2
  11P GAIN WILD-TYPE  126   54
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                3                126
  1                2                 54
[1] 2 2
[1] FALSE
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     3   1
  11P GAIN WILD-TYPE 105   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    1
  11P GAIN WILD-TYPE  105    9
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                3                105
  1                1                  9
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1   3
  11P GAIN WILD-TYPE  54 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    3
  11P GAIN WILD-TYPE   54  120
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 1                 54
  YES                3                120
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED               0                                7
  11P GAIN WILD-TYPE             6                              235
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11P GAIN MUTATED                                               0
  11P GAIN WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11P GAIN MUTATED                                     2
  11P GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11P GAIN MUTATED                                           0
  11P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11P GAIN MUTATED                                              0
  11P GAIN WILD-TYPE                                           17
D21V7, multiclass
                                               clus
vv                                              11P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             7
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              11P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             235
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 89 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A2LS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A7XC         TCGA-C5-A8XH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8XI         TCGA-C5-A8YQ         TCGA-C5-A8YT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8ZZ         TCGA-DG-A2KK         TCGA-DG-A2KL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-GH-A9DA         TCGA-HM-A4S6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-AAVH         TCGA-JX-A3Q0         TCGA-MA-AA3W 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MA-AA3X         TCGA-MA-AA41         TCGA-MA-AA43 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Q1-A73Q         TCGA-Q1-A73S         TCGA-RA-A741 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PG         TCGA-VS-A8EH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A8QM         TCGA-VS-A94Y         TCGA-VS-A94Z 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A9UP         TCGA-VS-A9UU         TCGA-VS-A9V0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A9V1         TCGA-VS-A9V4         TCGA-WL-A834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZJ-A8QQ         TCGA-ZJ-A8QR         TCGA-ZJ-AAX4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZJ-AAXA         TCGA-ZJ-AAXN         TCGA-ZJ-AAXT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZJ-AAXU         TCGA-ZJ-AB0I 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                8    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED                           1
  11P GAIN WILD-TYPE                        27
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           0     7
  11P GAIN WILD-TYPE                                         2   195
D21V10, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                1                 27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                    7                195
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1   3
  11P GAIN WILD-TYPE  22 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    3
  11P GAIN WILD-TYPE   22  159
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 22
  NOT HISPANIC OR LATINO                3                159
[1] 2 2
[1] FALSE
D21V12, continuous
D21V13, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5   3
  11P GAIN WILD-TYPE 178  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    3
  11P GAIN WILD-TYPE  178   71
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  TUMOR FREE                5                178
  WITH TUMOR                3                 71
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  11P GAIN MUTATED     0   3   5   0   0
  11P GAIN WILD-TYPE  18 126 110   1  24
D21V14, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  G1                0                 18
  G2                3                126
  G3                5                110
  G4                0                  1
  GX                0                 24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V15, continuous
D21V16, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 89 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A2LS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A7XC         TCGA-C5-A8XH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8XI         TCGA-C5-A8YQ         TCGA-C5-A8YT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8ZZ         TCGA-DG-A2KK         TCGA-DG-A2KL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-GH-A9DA         TCGA-HM-A4S6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-AAVH         TCGA-JX-A3Q0         TCGA-MA-AA3W 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MA-AA3X         TCGA-MA-AA41         TCGA-MA-AA43 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Q1-A73Q         TCGA-Q1-A73S         TCGA-RA-A741 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PG         TCGA-VS-A8EH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A8QM         TCGA-VS-A94Y         TCGA-VS-A94Z 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A9UP         TCGA-VS-A9UU         TCGA-VS-A9V0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A9V1         TCGA-VS-A9V4         TCGA-WL-A834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZJ-A8QQ         TCGA-ZJ-A8QR         TCGA-ZJ-AAX4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZJ-AAXA         TCGA-ZJ-AAXN         TCGA-ZJ-AAXT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZJ-AAXU         TCGA-ZJ-AB0I 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11P GAIN MUTATED                                             0
  11P GAIN WILD-TYPE                                          38
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  11P GAIN MUTATED                                        0
  11P GAIN WILD-TYPE                                      9
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  11P GAIN MUTATED                                                 1
  11P GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11P GAIN MUTATED                1                   3
  11P GAIN WILD-TYPE             61                 140
D21V17, multiclass
                                                 clus
vv                                                11P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 1
  LIFELONG NON-SMOKER                                            3
                                                 clus
vv                                                11P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     38
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  61
  LIFELONG NON-SMOKER                                            140
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V18, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 83 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A2LS         TCGA-C5-A2LV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LZ         TCGA-C5-A2M2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A8XI         TCGA-C5-A8YQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A8YT         TCGA-C5-A8ZZ         TCGA-C5-A907 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DR-A0ZM         TCGA-DS-A5RQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EK-A2RA         TCGA-EX-A1H5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3TX         TCGA-FU-A3WB 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A4S6         TCGA-HM-A6W2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VK         TCGA-JW-AAVH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-MA-AA3W         TCGA-MA-AA3X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MA-AA41         TCGA-MA-AA43         TCGA-MU-A5YI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-Q1-A73Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-UC-A7PD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PG         TCGA-VS-A8EH         TCGA-VS-A8QF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A8QM         TCGA-VS-A94Y         TCGA-VS-A94Z 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A9UP         TCGA-VS-A9UU         TCGA-VS-A9V0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A9V1         TCGA-VS-A9V4         TCGA-WL-A834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZJ-A8QQ         TCGA-ZJ-A8QR         TCGA-ZJ-AAX4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZJ-AAXA         TCGA-ZJ-AAXN         TCGA-ZJ-AAXT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZJ-AAXU         TCGA-ZJ-AB0I 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V19, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  0
  11P GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    0
  11P GAIN WILD-TYPE   23    3
                         clus
vv                        11P GAIN MUTATED 11P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   2                 23
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D21V20, continuous
D21V21, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                104 
        TCGA-2W-A8YY         TCGA-4J-AA1J         TCGA-BI-A0VR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BI-A0VS         TCGA-C5-A1BE         TCGA-C5-A1BI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BK         TCGA-C5-A1BL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M6         TCGA-C5-A1M7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1ME         TCGA-C5-A1MF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1ML         TCGA-C5-A1MN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A2LS         TCGA-C5-A2LV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A2M2         TCGA-C5-A3HD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A3HE         TCGA-C5-A3HF         TCGA-C5-A3HL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CH         TCGA-C5-A7CJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UH         TCGA-C5-A7X3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A8ZZ         TCGA-DG-A2KL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A5RQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A3QD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A3Y4         TCGA-EA-A410 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A44S         TCGA-EA-A556 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EX-A449         TCGA-FU-A2QG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A770         TCGA-HG-A2PA 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-IR-A3L7         TCGA-IR-A3LC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-IR-A3LI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-IR-A3LL         TCGA-JW-A5VG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A5VH         TCGA-JW-A5VI         TCGA-JW-A5VJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-JW-A5VL         TCGA-JW-A69B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3PZ         TCGA-JX-A3Q0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-JX-A5QV         TCGA-RA-A741 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF         TCGA-UC-A7PG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PI         TCGA-ZX-AA5X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V22, continuous
D21V23, continuous
D21V24, continuous
D21V25, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                108 
        TCGA-2W-A8YY         TCGA-4J-AA1J         TCGA-BI-A0VR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BI-A0VS         TCGA-C5-A1BE         TCGA-C5-A1BI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BK         TCGA-C5-A1BL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M6         TCGA-C5-A1M7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1ME         TCGA-C5-A1MF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1ML         TCGA-C5-A1MN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A2LS         TCGA-C5-A2LV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A2M2         TCGA-C5-A3HD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A3HE         TCGA-C5-A3HF         TCGA-C5-A3HL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CH         TCGA-C5-A7CJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UH         TCGA-C5-A7X3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A8ZZ         TCGA-DG-A2KL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A5RQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A3QD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A3Y4         TCGA-EA-A410 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A44S         TCGA-EA-A556 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EX-A69M         TCGA-FU-A2QG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A5XV         TCGA-FU-A770 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK         TCGA-IR-A3L7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3LC         TCGA-IR-A3LF         TCGA-IR-A3LH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-IR-A3LL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A5VG         TCGA-JW-A5VH         TCGA-JW-A5VI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A5VL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-JX-A3PZ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MA-AA3W         TCGA-Q1-A73Q         TCGA-RA-A741 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF         TCGA-UC-A7PG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PI         TCGA-XS-A8TJ         TCGA-ZX-AA5X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  11P GAIN MUTATED                                     0
  11P GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  11P GAIN MUTATED                                     0
  11P GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  11P GAIN MUTATED                         2                       0
  11P GAIN WILD-TYPE                      34                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11P GAIN MUTATED                         0
  11P GAIN WILD-TYPE                       8
D21V26, multiclass
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 53 
        TCGA-2W-A8YY         TCGA-BI-A20A         TCGA-C5-A0TN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BE         TCGA-C5-A1BK         TCGA-C5-A1BM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M7         TCGA-C5-A1M8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A2LS         TCGA-C5-A2LV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2M1         TCGA-C5-A3HE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7UC         TCGA-C5-A7UI         TCGA-C5-A7X8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7XC         TCGA-C5-A8XH         TCGA-C5-A8XI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DG-A2KL         TCGA-DR-A0ZM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A50E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EK-A2RN         TCGA-EK-A2RO         TCGA-EX-A1H5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EX-A449         TCGA-FU-A3EO         TCGA-HM-A4S6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-UC-A7PD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-VS-A8QA         TCGA-VS-A9UT         TCGA-WL-A834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-XS-A8TJ         TCGA-ZJ-AAX4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  11P GAIN MUTATED                                               0
  11P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  11P GAIN MUTATED                                                1
  11P GAIN WILD-TYPE                                             24
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11P GAIN MUTATED                                                                                   0
  11P GAIN WILD-TYPE                                                                                82
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11P GAIN MUTATED                                                                                              6
  11P GAIN WILD-TYPE                                                                                          115
D21V27, multiclass
                                                                                              clus
vv                                                                                             11P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           0
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                6
                                                                                              clus
vv                                                                                             11P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            82
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V28, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  2
  11P GAIN WILD-TYPE 68 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    2
  11P GAIN WILD-TYPE   68   72
         clus
vv        11P GAIN MUTATED 11P GAIN WILD-TYPE
  ABSENT                 3                 68
  PRESENT                2                 72
[1] 2 2
[1] FALSE
D21V29, continuous
D21V30, continuous
D21V31, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1   2
  11P GAIN WILD-TYPE  48 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    2
  11P GAIN WILD-TYPE   48  115
                                          clus
vv                                         11P GAIN MUTATED 11P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    1                 48
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                2                115
[1] 2 2
[1] FALSE
D21V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11P GAIN MUTATED              1           3          0
  11P GAIN WILD-TYPE           14          51         85
D21V33, multiclass
              clus
vv             11P GAIN MUTATED 11P GAIN WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 3                 51
  NEVER USED                  0                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V34, continuous
D21V35, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  0
  11P GAIN WILD-TYPE 89 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    0
  11P GAIN WILD-TYPE   89   18
         clus
vv        11P GAIN MUTATED 11P GAIN WILD-TYPE
  ABSENT                 3                 89
  PRESENT                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  11P GAIN MUTATED             0         3     1
  11P GAIN WILD-TYPE           5        97     1
D21V36, multiclass
             clus
vv            11P GAIN MUTATED 11P GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                  3                 97
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V37, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A3JK         TCGA-JW-A852 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-MA-AA3W         TCGA-MA-AA3Z 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MA-AA42         TCGA-MU-A51Y         TCGA-MU-A8JM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ZX-AA5X 
"11P GAIN WILD-TYPE" 
D21V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  11P GAIN MUTATED         0        0         0         0        2         1
  11P GAIN WILD-TYPE       5        1         1         1       32        76
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  11P GAIN MUTATED           1        0         1          0          0
  11P GAIN WILD-TYPE        36        4         7          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  11P GAIN MUTATED           0         0          0          3         0
  11P GAIN WILD-TYPE        44         1          3         39         7
                    vv
clus                 STAGE IVB
  11P GAIN MUTATED           0
  11P GAIN WILD-TYPE        12
D21V39, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  2                 32
  STAGE IB1                 1                 76
  STAGE IB2                 1                 36
  STAGE II                  0                  4
  STAGE IIA                 1                  7
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 0                 44
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB                3                 39
  STAGE IVA                 0                  7
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     5   1
  11Q GAIN WILD-TYPE 206  66
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                272 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 66 
$`11Q GAIN MUTATED`
TCGA-C5-A1M9 TCGA-C5-A2LT TCGA-DG-A2KJ TCGA-EK-A2H1 TCGA-FU-A40J TCGA-MY-A913 
       35.01        73.18        95.11        26.27        14.01        17.23 

$`11Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       30.21        57.73        53.16        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
        2.43        20.91        40.93         3.58        44.22        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      131.11        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       45.83         8.35       146.86        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
       20.81        20.91        14.73         1.12        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63        69.96 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       95.67        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
        0.36        12.59        60.72         6.64         1.51        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
       40.96         4.31         0.10         0.43        47.77         0.53 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.49         0.76         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       15.22        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
       26.14         1.48        16.14        28.31        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12        17.75        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        8.28        18.15        21.11       209.59        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        19.56        17.82        19.56         8.35         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       22.62        19.59        14.60        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       69.50        10.03        46.52        45.57        32.42        23.97 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       19.96        65.49        32.15        53.59        36.13        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       59.18        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       33.37        40.14        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       29.95        27.12        24.30        46.92        45.11         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       14.53        27.25        47.87        47.47        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       15.85        14.53         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 
        5.16        18.25        17.75         4.34        16.24        15.42 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       26.01        29.26        67.59        19.13         0.69         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             14.01               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             95.11             210.67 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             30.64              22.80 
[1] "14.0 - 95.1 (30.6)" "0.0 - 210.7 (22.8)"
[1] "hr=" "1.9"
D22V2, continuous
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED     3   1   1   0
  11Q GAIN WILD-TYPE 132  69  20   8
D22V3, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                3                132
  T2                1                 69
  T3                1                 20
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3   3
  11Q GAIN WILD-TYPE 126  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    3
  11Q GAIN WILD-TYPE  126   53
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                3                126
  1                3                 53
[1] 2 2
[1] FALSE
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3   1
  11Q GAIN WILD-TYPE 105   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    1
  11Q GAIN WILD-TYPE  105    9
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                3                105
  1                1                  9
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   2
  11Q GAIN WILD-TYPE  55 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    2
  11Q GAIN WILD-TYPE   55  121
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                 55
  YES                2                121
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED               0                                6
  11Q GAIN WILD-TYPE             6                              236
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11Q GAIN MUTATED                                               0
  11Q GAIN WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11Q GAIN MUTATED                                     2
  11Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11Q GAIN MUTATED                                           0
  11Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11Q GAIN MUTATED                                              0
  11Q GAIN WILD-TYPE                                           17
D22V7, multiclass
                                               clus
vv                                              11Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             6
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              11Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             236
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 89 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A2LS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A7XC         TCGA-C5-A8XH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8XI         TCGA-C5-A8YQ         TCGA-C5-A8YT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8ZZ         TCGA-DG-A2KK         TCGA-DG-A2KL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-GH-A9DA         TCGA-HM-A4S6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-AAVH         TCGA-JX-A3Q0         TCGA-MA-AA3W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MA-AA3X         TCGA-MA-AA41         TCGA-MA-AA43 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Q1-A73Q         TCGA-Q1-A73S         TCGA-RA-A741 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PG         TCGA-VS-A8EH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8QM         TCGA-VS-A94Y         TCGA-VS-A94Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9UP         TCGA-VS-A9UU         TCGA-VS-A9V0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9V1         TCGA-VS-A9V4         TCGA-WL-A834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZJ-A8QQ         TCGA-ZJ-A8QR         TCGA-ZJ-AAX4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZJ-AAXA         TCGA-ZJ-AAXN         TCGA-ZJ-AAXT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZJ-AAXU         TCGA-ZJ-AB0I 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                8    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED                           1
  11Q GAIN WILD-TYPE                        27
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           0     5
  11Q GAIN WILD-TYPE                                         2   197
D22V10, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                1                 27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                    5                197
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1   4
  11Q GAIN WILD-TYPE  22 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    4
  11Q GAIN WILD-TYPE   22  158
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 22
  NOT HISPANIC OR LATINO                4                158
[1] 2 2
[1] FALSE
D22V12, continuous
D22V13, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     5   1
  11Q GAIN WILD-TYPE 178  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    1
  11Q GAIN WILD-TYPE  178   73
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  TUMOR FREE                5                178
  WITH TUMOR                1                 73
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  11Q GAIN MUTATED     0   0   7   0   0
  11Q GAIN WILD-TYPE  18 129 108   1  24
D22V14, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  G1                0                 18
  G2                0                129
  G3                7                108
  G4                0                  1
  GX                0                 24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V15, continuous
D22V16, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 89 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1ML         TCGA-C5-A1MN         TCGA-C5-A2LS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A7XC         TCGA-C5-A8XH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8XI         TCGA-C5-A8YQ         TCGA-C5-A8YT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8ZZ         TCGA-DG-A2KK         TCGA-DG-A2KL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-GH-A9DA         TCGA-HM-A4S6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-AAVH         TCGA-JX-A3Q0         TCGA-MA-AA3W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MA-AA3X         TCGA-MA-AA41         TCGA-MA-AA43 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Q1-A73Q         TCGA-Q1-A73S         TCGA-RA-A741 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PG         TCGA-VS-A8EH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8QM         TCGA-VS-A94Y         TCGA-VS-A94Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9UP         TCGA-VS-A9UU         TCGA-VS-A9V0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9V1         TCGA-VS-A9V4         TCGA-WL-A834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZJ-A8QQ         TCGA-ZJ-A8QR         TCGA-ZJ-AAX4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZJ-AAXA         TCGA-ZJ-AAXN         TCGA-ZJ-AAXT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZJ-AAXU         TCGA-ZJ-AB0I 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11Q GAIN MUTATED                                             0
  11Q GAIN WILD-TYPE                                          38
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  11Q GAIN MUTATED                                        0
  11Q GAIN WILD-TYPE                                      9
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  11Q GAIN MUTATED                                                 1
  11Q GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11Q GAIN MUTATED                1                   2
  11Q GAIN WILD-TYPE             61                 141
D22V17, multiclass
                                                 clus
vv                                                11Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 1
  LIFELONG NON-SMOKER                                            2
                                                 clus
vv                                                11Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     38
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  61
  LIFELONG NON-SMOKER                                            141
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V18, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 83 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A2LS         TCGA-C5-A2LV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LZ         TCGA-C5-A2M2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A8XI         TCGA-C5-A8YQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8YT         TCGA-C5-A8ZZ         TCGA-C5-A907 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DR-A0ZM         TCGA-DS-A5RQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EK-A2RA         TCGA-EX-A1H5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3TX         TCGA-FU-A3WB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A4S6         TCGA-HM-A6W2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VK         TCGA-JW-AAVH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-MA-AA3W         TCGA-MA-AA3X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MA-AA41         TCGA-MA-AA43         TCGA-MU-A5YI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-Q1-A73Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-UC-A7PD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PG         TCGA-VS-A8EH         TCGA-VS-A8QF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8QM         TCGA-VS-A94Y         TCGA-VS-A94Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9UP         TCGA-VS-A9UU         TCGA-VS-A9V0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9V1         TCGA-VS-A9V4         TCGA-WL-A834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZJ-A8QQ         TCGA-ZJ-A8QR         TCGA-ZJ-AAX4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZJ-AAXA         TCGA-ZJ-AAXN         TCGA-ZJ-AAXT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZJ-AAXU         TCGA-ZJ-AB0I 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V19, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  0
  11Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    0
  11Q GAIN WILD-TYPE   23    3
                         clus
vv                        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   2                 23
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D22V20, continuous
D22V21, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                104 
        TCGA-2W-A8YY         TCGA-4J-AA1J         TCGA-BI-A0VR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BI-A0VS         TCGA-C5-A1BE         TCGA-C5-A1BI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BK         TCGA-C5-A1BL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M6         TCGA-C5-A1M7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1ME         TCGA-C5-A1MF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1ML         TCGA-C5-A1MN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A2LS         TCGA-C5-A2LV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A2M2         TCGA-C5-A3HD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A3HE         TCGA-C5-A3HF         TCGA-C5-A3HL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CH         TCGA-C5-A7CJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UH         TCGA-C5-A7X3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A8ZZ         TCGA-DG-A2KL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A5RQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A3QD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A3Y4         TCGA-EA-A410 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A44S         TCGA-EA-A556 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EX-A449         TCGA-FU-A2QG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A770         TCGA-HG-A2PA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-IR-A3L7         TCGA-IR-A3LC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-IR-A3LI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-IR-A3LL         TCGA-JW-A5VG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VH         TCGA-JW-A5VI         TCGA-JW-A5VJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-JW-A5VL         TCGA-JW-A69B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3PZ         TCGA-JX-A3Q0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-JX-A5QV         TCGA-RA-A741 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF         TCGA-UC-A7PG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PI         TCGA-ZX-AA5X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V22, continuous
D22V23, continuous
D22V24, continuous
D22V25, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                108 
        TCGA-2W-A8YY         TCGA-4J-AA1J         TCGA-BI-A0VR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BI-A0VS         TCGA-C5-A1BE         TCGA-C5-A1BI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BK         TCGA-C5-A1BL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M6         TCGA-C5-A1M7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1M8         TCGA-C5-A1ME         TCGA-C5-A1MF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1ML         TCGA-C5-A1MN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A2LS         TCGA-C5-A2LV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A2M2         TCGA-C5-A3HD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A3HE         TCGA-C5-A3HF         TCGA-C5-A3HL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CH         TCGA-C5-A7CJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UH         TCGA-C5-A7X3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-C5-A8ZZ         TCGA-DG-A2KL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A5RQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A3QD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A3Y4         TCGA-EA-A410 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A44S         TCGA-EA-A556 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EX-A69M         TCGA-FU-A2QG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A5XV         TCGA-FU-A770 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK         TCGA-IR-A3L7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LC         TCGA-IR-A3LF         TCGA-IR-A3LH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-IR-A3LL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VG         TCGA-JW-A5VH         TCGA-JW-A5VI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A5VL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-JX-A3PZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A3Q0         TCGA-JX-A3Q8         TCGA-JX-A5QV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MA-AA3W         TCGA-Q1-A73Q         TCGA-RA-A741 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF         TCGA-UC-A7PG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PI         TCGA-XS-A8TJ         TCGA-ZX-AA5X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  11Q GAIN MUTATED                                     0
  11Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  11Q GAIN MUTATED                                     0
  11Q GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  11Q GAIN MUTATED                         2                       0
  11Q GAIN WILD-TYPE                      34                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11Q GAIN MUTATED                         0
  11Q GAIN WILD-TYPE                       8
D22V26, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 53 
        TCGA-2W-A8YY         TCGA-BI-A20A         TCGA-C5-A0TN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BE         TCGA-C5-A1BK         TCGA-C5-A1BM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M7         TCGA-C5-A1M8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-C5-A2LS         TCGA-C5-A2LV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2M1         TCGA-C5-A3HE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7UC         TCGA-C5-A7UI         TCGA-C5-A7X8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7XC         TCGA-C5-A8XH         TCGA-C5-A8XI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DG-A2KK         TCGA-DG-A2KL         TCGA-DR-A0ZM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A50E 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EK-A2RN         TCGA-EK-A2RO         TCGA-EX-A1H5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EX-A449         TCGA-FU-A3EO         TCGA-HM-A4S6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-UC-A7PD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8QA         TCGA-VS-A9UT         TCGA-WL-A834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-XS-A8TJ         TCGA-ZJ-AAX4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  11Q GAIN MUTATED                                               0
  11Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  11Q GAIN MUTATED                                                0
  11Q GAIN WILD-TYPE                                             25
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11Q GAIN MUTATED                                                                                   0
  11Q GAIN WILD-TYPE                                                                                82
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11Q GAIN MUTATED                                                                                              5
  11Q GAIN WILD-TYPE                                                                                          116
D22V27, multiclass
                                                                                              clus
vv                                                                                             11Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           0
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                5
                                                                                              clus
vv                                                                                             11Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               25
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            82
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V28, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  3
  11Q GAIN WILD-TYPE 69 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    3
  11Q GAIN WILD-TYPE   69   71
         clus
vv        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ABSENT                 2                 69
  PRESENT                3                 71
[1] 2 2
[1] FALSE
D22V29, continuous
D22V30, continuous
D22V31, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1   4
  11Q GAIN WILD-TYPE  48 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    4
  11Q GAIN WILD-TYPE   48  113
                                          clus
vv                                         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    1                 48
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                4                113
[1] 2 2
[1] FALSE
D22V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11Q GAIN MUTATED              1           1          0
  11Q GAIN WILD-TYPE           14          53         85
D22V33, multiclass
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                152 
        TCGA-2W-A8YY         TCGA-4J-AA1J         TCGA-C5-A1BI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1M6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         TCGA-C5-A1ME 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MN         TCGA-C5-A2LV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2M1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7UH         TCGA-C5-A7X3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A8YT         TCGA-DG-A2KM         TCGA-DR-A0ZL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HS         TCGA-EA-A3HT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3QE         TCGA-EA-A410 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A43B         TCGA-EA-A44S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A4BA         TCGA-EA-A50E         TCGA-EA-A556 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EA-A5ZE         TCGA-EA-A5ZF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A97N         TCGA-EK-A2R7         TCGA-EK-A3GK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A1H6         TCGA-EX-A3L1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EX-A69L         TCGA-EX-A69M         TCGA-FU-A2QG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3WB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A57G         TCGA-FU-A770 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HG-A9SC         TCGA-HM-A3JJ         TCGA-HM-A3JK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LA         TCGA-IR-A3LB         TCGA-IR-A3LC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-IR-A3LI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-JW-A5VG         TCGA-JW-A5VI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A69B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A3PZ         TCGA-JX-A3Q0         TCGA-JX-A3Q8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A5QV         TCGA-LP-A5U2         TCGA-LP-A5U3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-LP-A7HU         TCGA-MA-AA3Y         TCGA-MA-AA3Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MA-AA41         TCGA-MA-AA43         TCGA-PN-A8MA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Q1-A5R1         TCGA-Q1-A5R2         TCGA-Q1-A5R3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DV         TCGA-Q1-A73P         TCGA-Q1-A73S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PI         TCGA-VS-A8EB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8EC         TCGA-VS-A8EG         TCGA-VS-A8EH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A8EI         TCGA-VS-A8EL         TCGA-VS-A8Q8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A94W         TCGA-VS-A94Y         TCGA-VS-A94Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A950         TCGA-VS-A952         TCGA-VS-A953 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A954         TCGA-VS-A957         TCGA-VS-A958 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A959         TCGA-VS-A9U5         TCGA-VS-A9U6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9U7         TCGA-VS-A9UA         TCGA-VS-A9UB 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9UC         TCGA-VS-A9UD         TCGA-VS-A9UH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9UI         TCGA-VS-A9UJ         TCGA-VS-A9UL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9UM         TCGA-VS-A9UO         TCGA-VS-A9UP 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9UQ         TCGA-VS-A9UR         TCGA-VS-A9UT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9UU         TCGA-VS-A9UV         TCGA-VS-A9UZ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9V0         TCGA-VS-A9V1         TCGA-VS-A9V2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-VS-A9V3         TCGA-VS-A9V5         TCGA-VS-AA62 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-WL-A834         TCGA-XS-A8TJ         TCGA-ZJ-A8QQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZJ-AAX4         TCGA-ZJ-AB0I 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V34, continuous
D22V35, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    4  0
  11Q GAIN WILD-TYPE 88 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4    0
  11Q GAIN WILD-TYPE   88   18
         clus
vv        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ABSENT                 4                 88
  PRESENT                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  11Q GAIN MUTATED             0         4     1
  11Q GAIN WILD-TYPE           5        96     1
D22V36, multiclass
             clus
vv            11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                  4                 96
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V37, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A3JK         TCGA-JW-A852 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-MA-AA3W         TCGA-MA-AA3Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MA-AA42         TCGA-MU-A51Y         TCGA-MU-A8JM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ZX-AA5X 
"11Q GAIN WILD-TYPE" 
D22V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  11Q GAIN MUTATED         0        0         0         0        1         1
  11Q GAIN WILD-TYPE       5        1         1         1       33        76
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  11Q GAIN MUTATED           2        0         1          0          0
  11Q GAIN WILD-TYPE        35        4         7          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  11Q GAIN MUTATED           0         0          0          2         0
  11Q GAIN WILD-TYPE        44         1          3         40         7
                    vv
clus                 STAGE IVB
  11Q GAIN MUTATED           0
  11Q GAIN WILD-TYPE        12
D22V39, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  1                 33
  STAGE IB1                 1                 76
  STAGE IB2                 2                 35
  STAGE II                  0                  4
  STAGE IIA                 1                  7
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 0                 44
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB                2                 40
  STAGE IVA                 0                  7
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    37  13
  12P GAIN WILD-TYPE 174  54
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                50                228 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                13                 54 
$`12P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       57.04        31.40        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CH 
        0.46        73.18        83.05        18.02       210.67       154.32 
TCGA-C5-A7CK TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-DG-A2KL 
      134.33         9.34        13.61         8.35        23.51        44.94 
TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N 
       22.98        39.55        31.73        25.91        27.22         0.36 
TCGA-EK-A2R8 TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A5XV 
        1.45        23.84        16.11        20.98         1.48        10.55 
TCGA-GH-A9DA TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MA-AA41 TCGA-MU-A8JM 
       17.75        20.91         0.30        13.35         8.35        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC 
       54.81        35.05        17.23        12.16        10.03        46.52 
TCGA-VS-A8EJ TCGA-VS-A94X TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH 
       19.96        16.64        50.47        28.50        24.30        46.92 
TCGA-VS-A9UP TCGA-VS-A9V0 
       47.47        18.84 

$`12P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
        5.46        19.86        67.46        46.32        30.21        35.01 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
        2.43        20.91        40.93         3.58        44.22        73.45 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF 
       78.35       100.14        38.43        33.24        52.01        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
       20.42       101.82        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
      155.77       131.11        94.95         2.73        50.99        45.83 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
      146.86        99.91        27.52        20.81        20.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        95.11        82.06        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76        55.63        69.96        95.67        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52         8.28        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       27.29        27.25        24.00        13.48        12.59        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL 
       26.27         6.64         1.51        19.27         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         0.36         0.13        40.96         4.31         0.10 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM 
        0.43        47.77         0.53         0.10         0.49         0.76 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92        15.22        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
        8.32        15.55         1.22        19.04        31.36        36.26 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 
       26.14        16.14        28.31        14.01        35.44         1.12 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41        16.57        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        44.61        11.28         0.89        12.49 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 
        0.82        22.52        19.56        17.82        19.56         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
       11.38        28.08        34.62        20.84         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       11.67        93.99        69.50        45.57        32.42        23.97 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       65.49        32.15        53.59        36.13        11.51        59.18 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       39.78        31.27        40.87         4.73        33.37        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       58.45        15.68        56.35        55.50        50.14        51.32 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UJ 
       43.40        48.39        29.95        27.12        45.11         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       14.53        27.25        47.87        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 
       14.53         3.42        18.25        67.20         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       17.75         4.34        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         0.69         1.41         0.16         3.91 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.30               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            210.67             209.59 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            23.675             22.570 
[1] "0.3 - 210.7 (23.7)" "0.0 - 209.6 (22.6)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED    22  14   8   1
  12P GAIN WILD-TYPE 113  56  13   7
D23V3, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               22                113
  T2               14                 56
  T3                8                 13
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    25  10
  12P GAIN WILD-TYPE 104  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     25   10
  12P GAIN WILD-TYPE  104   46
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               25                104
  1               10                 46
[1] 2 2
[1] FALSE
D23V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   20  4
  12P GAIN WILD-TYPE 88  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     20    4
  12P GAIN WILD-TYPE   88    6
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               20                 88
  1                4                  6
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    9 24
  12P GAIN WILD-TYPE 46 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      9   24
  12P GAIN WILD-TYPE   46   99
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 9                 46
  YES               24                 99
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED               0                               46
  12P GAIN WILD-TYPE             6                              196
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12P GAIN MUTATED                                               1
  12P GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12P GAIN MUTATED                                     4
  12P GAIN WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12P GAIN MUTATED                                           0
  12P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12P GAIN MUTATED                                              2
  12P GAIN WILD-TYPE                                           15
D23V7, multiclass
                                               clus
vv                                              12P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            46
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              12P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             196
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, continuous
D23V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     4
  12P GAIN WILD-TYPE                                8    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED                           6
  12P GAIN WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           0    35
  12P GAIN WILD-TYPE                                         2   167
D23V10, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                                6                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   35                167
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     3  28
  12P GAIN WILD-TYPE  20 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   28
  12P GAIN WILD-TYPE   20  134
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 20
  NOT HISPANIC OR LATINO               28                134
[1] 2 2
[1] FALSE
D23V12, continuous
D23V13, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    34  14
  12P GAIN WILD-TYPE 149  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     34   14
  12P GAIN WILD-TYPE  149   60
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  TUMOR FREE               34                149
  WITH TUMOR               14                 60
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  12P GAIN MUTATED     4  21  25   0   2
  12P GAIN WILD-TYPE  14 108  90   1  22
D23V14, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  G1                4                 14
  G2               21                108
  G3               25                 90
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, continuous
D23V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  12P GAIN MUTATED                                             5
  12P GAIN WILD-TYPE                                          33
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  12P GAIN MUTATED                                        2
  12P GAIN WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  12P GAIN MUTATED                                                 2
  12P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12P GAIN MUTATED               15                  23
  12P GAIN WILD-TYPE             47                 120
D23V17, multiclass
                                                 clus
vv                                                12P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                2
  CURRENT SMOKER                                                15
  LIFELONG NON-SMOKER                                           23
                                                 clus
vv                                                12P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  47
  LIFELONG NON-SMOKER                                            120
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V18, continuous
D23V19, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    7  0
  12P GAIN WILD-TYPE 18  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7    0
  12P GAIN WILD-TYPE   18    3
                         clus
vv                        12P GAIN MUTATED 12P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   7                 18
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D23V20, continuous
D23V21, continuous
D23V22, continuous
D23V23, continuous
D23V24, continuous
D23V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  12P GAIN MUTATED                                     0
  12P GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  12P GAIN MUTATED                                     1
  12P GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  12P GAIN MUTATED                         8                       0
  12P GAIN WILD-TYPE                      28                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12P GAIN MUTATED                         3
  12P GAIN WILD-TYPE                       5
D23V26, multiclass
                                     clus
vv                                    12P GAIN MUTATED 12P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                            8                 28
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  12P GAIN MUTATED                                               0
  12P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12P GAIN MUTATED                                                5
  12P GAIN WILD-TYPE                                             20
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12P GAIN MUTATED                                                                                  17
  12P GAIN WILD-TYPE                                                                                65
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12P GAIN MUTATED                                                                                             18
  12P GAIN WILD-TYPE                                                                                          103
D23V27, multiclass
                                                                                              clus
vv                                                                                             12P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               18
                                                                                              clus
vv                                                                                             12P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V28, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   15 12
  12P GAIN WILD-TYPE 56 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     15   12
  12P GAIN WILD-TYPE   56   62
         clus
vv        12P GAIN MUTATED 12P GAIN WILD-TYPE
  ABSENT                15                 56
  PRESENT               12                 62
[1] 2 2
[1] FALSE
D23V29, continuous
D23V30, continuous
D23V31, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    15  17
  12P GAIN WILD-TYPE  34 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     15   17
  12P GAIN WILD-TYPE   34  100
                                          clus
vv                                         12P GAIN MUTATED 12P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   15                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               17                100
[1] 2 2
[1] FALSE
D23V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12P GAIN MUTATED              1           9         15
  12P GAIN WILD-TYPE           14          45         70
D23V33, multiclass
              clus
vv             12P GAIN MUTATED 12P GAIN WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 9                 45
  NEVER USED                 15                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V34, continuous
D23V35, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   17  3
  12P GAIN WILD-TYPE 75 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     17    3
  12P GAIN WILD-TYPE   75   15
         clus
vv        12P GAIN MUTATED 12P GAIN WILD-TYPE
  ABSENT                17                 75
  PRESENT                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  12P GAIN MUTATED             1        19     0
  12P GAIN WILD-TYPE           4        81     2
D23V36, multiclass
             clus
vv            12P GAIN MUTATED 12P GAIN WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 19                 81
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V37, continuous
D23V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  12P GAIN MUTATED         0        0         0         0        4        12
  12P GAIN WILD-TYPE       5        1         1         1       30        65
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  12P GAIN MUTATED           7        1         3          2          0
  12P GAIN WILD-TYPE        30        3         5          3          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  12P GAIN MUTATED           9         0          2         10         2
  12P GAIN WILD-TYPE        35         1          1         32         5
                    vv
clus                 STAGE IVB
  12P GAIN MUTATED           1
  12P GAIN WILD-TYPE        11
D23V39, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  4                 30
  STAGE IB1                12                 65
  STAGE IB2                 7                 30
  STAGE II                  1                  3
  STAGE IIA                 3                  5
  STAGE IIA1                2                  3
  STAGE IIA2                0                  7
  STAGE IIB                 9                 35
  STAGE III                 0                  1
  STAGE IIIA                2                  1
  STAGE IIIB               10                 32
  STAGE IVA                 2                  5
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    36  11
  12Q GAIN WILD-TYPE 175  56
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                47                231 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                11                 56 
$`12Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       57.04        31.40        53.16        38.99        35.61         0.46 
TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CK 
       73.18        83.05        52.01        18.02       210.67       134.33 
TCGA-C5-A7X3 TCGA-C5-A8XH TCGA-C5-A8XI TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A3LQ 
        9.34        45.83         8.35        95.11        44.94        22.98 
TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2R8 TCGA-FU-A23L 
       39.55        31.73        27.22         0.36         1.45        23.84 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A5XV TCGA-GH-A9DA TCGA-JX-A5QV TCGA-LP-A5U2 
       20.98         1.48        10.55        17.75        20.91         0.30 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA41 TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       13.35        22.52         8.35        19.96        54.81        35.05 
TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A94X 
       17.23        15.95        12.16        46.52        19.96        16.64 
TCGA-VS-A9U5 TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UP TCGA-VS-A9V0 
       50.47        29.95        24.30        47.47        18.84 

$`12Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
        5.46        19.86        67.46        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       57.73         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF 
       73.45        78.35       100.14        38.43        33.24        17.85 
TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       20.42       154.32       101.82        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 
       17.19       155.77       131.11        94.95        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
       50.99       146.86        99.91        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.91        14.73         1.12        82.06        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        36.76        55.63        69.96        95.67        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18        17.52         8.28        40.87        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       24.56        26.01         0.30        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
       26.79        25.91        27.29        27.25        24.00        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        60.72        26.27         6.64         1.51        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.39         0.43         0.59         0.36         0.13        40.96 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ 
        4.31         0.10         0.43        47.77         0.53         0.10 
TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.49         0.76         0.03        20.35         7.92        15.22 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
       14.70        19.79         8.32        15.55         1.22        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       16.11        31.36        36.26        26.14        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       14.01        35.44         1.12        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       209.59        44.61 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA3Y 
       11.28         0.89        12.49         0.82        19.56        17.82 
TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BF 
       19.56         8.52        11.38        28.08        34.62        20.84 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96        15.58        16.41         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
       14.60        11.67        93.99        69.50        10.03        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       32.42        23.97        65.49        32.15        53.59        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Y 
       11.51        59.18        39.78        31.27        40.87         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       33.37        40.14        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UC 
       50.14        51.32        43.40        48.39        28.50        27.12 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       46.92        45.11         1.71        14.53        27.25        47.87 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       41.52        26.07        15.85        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       67.20         5.16        18.25        17.75         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.30               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            210.67             209.59 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             23.84              22.62 
[1] "0.3 - 210.7 (23.8)" "0.0 - 209.6 (22.6)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED    23  14   6   0
  12Q GAIN WILD-TYPE 112  56  15   8
D24V3, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               23                112
  T2               14                 56
  T3                6                 15
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    24  12
  12Q GAIN WILD-TYPE 105  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     24   12
  12Q GAIN WILD-TYPE  105   44
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               24                105
  1               12                 44
[1] 2 2
[1] FALSE
D24V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   20  3
  12Q GAIN WILD-TYPE 88  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     20    3
  12Q GAIN WILD-TYPE   88    7
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               20                 88
  1                3                  7
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    10  21
  12Q GAIN WILD-TYPE  45 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     10   21
  12Q GAIN WILD-TYPE   45  102
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                10                 45
  YES               21                102
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED               0                               45
  12Q GAIN WILD-TYPE             6                              197
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12Q GAIN MUTATED                                               1
  12Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12Q GAIN MUTATED                                     2
  12Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12Q GAIN MUTATED                                           0
  12Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12Q GAIN MUTATED                                              2
  12Q GAIN WILD-TYPE                                           15
D24V7, multiclass
                                               clus
vv                                              12Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            45
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              12Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             197
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, continuous
D24V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     4
  12Q GAIN WILD-TYPE                                8    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED                           4
  12Q GAIN WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           0    32
  12Q GAIN WILD-TYPE                                         2   170
D24V10, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                                4                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   32                170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4  25
  12Q GAIN WILD-TYPE  19 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4   25
  12Q GAIN WILD-TYPE   19  137
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 19
  NOT HISPANIC OR LATINO               25                137
[1] 2 2
[1] FALSE
D24V12, continuous
D24V13, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    34  11
  12Q GAIN WILD-TYPE 149  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     34   11
  12Q GAIN WILD-TYPE  149   63
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  TUMOR FREE               34                149
  WITH TUMOR               11                 63
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  12Q GAIN MUTATED     3  19  26   0   0
  12Q GAIN WILD-TYPE  15 110  89   1  24
D24V14, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  G1                3                 15
  G2               19                110
  G3               26                 89
  G4                0                  1
  GX                0                 24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, continuous
D24V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  12Q GAIN MUTATED                                             6
  12Q GAIN WILD-TYPE                                          32
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  12Q GAIN MUTATED                                        2
  12Q GAIN WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  12Q GAIN MUTATED                                                 2
  12Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12Q GAIN MUTATED               13                  21
  12Q GAIN WILD-TYPE             49                 122
D24V17, multiclass
                                                 clus
vv                                                12Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                2
  CURRENT SMOKER                                                13
  LIFELONG NON-SMOKER                                           21
                                                 clus
vv                                                12Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  49
  LIFELONG NON-SMOKER                                            122
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V18, continuous
D24V19, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8  0
  12Q GAIN WILD-TYPE 17  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8    0
  12Q GAIN WILD-TYPE   17    3
                         clus
vv                        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   8                 17
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D24V20, continuous
D24V21, continuous
D24V22, continuous
D24V23, continuous
D24V24, continuous
D24V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  12Q GAIN MUTATED                                     0
  12Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  12Q GAIN MUTATED                                     1
  12Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  12Q GAIN MUTATED                         8                       0
  12Q GAIN WILD-TYPE                      28                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12Q GAIN MUTATED                         2
  12Q GAIN WILD-TYPE                       6
D24V26, multiclass
                                     clus
vv                                    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                            8                 28
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  12Q GAIN MUTATED                                               0
  12Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12Q GAIN MUTATED                                                5
  12Q GAIN WILD-TYPE                                             20
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12Q GAIN MUTATED                                                                                  17
  12Q GAIN WILD-TYPE                                                                                65
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12Q GAIN MUTATED                                                                                             15
  12Q GAIN WILD-TYPE                                                                                          106
D24V27, multiclass
                                                                                              clus
vv                                                                                             12Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               15
                                                                                              clus
vv                                                                                             12Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V28, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   12 12
  12Q GAIN WILD-TYPE 59 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12   12
  12Q GAIN WILD-TYPE   59   62
         clus
vv        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ABSENT                12                 59
  PRESENT               12                 62
[1] 2 2
[1] FALSE
D24V29, continuous
D24V30, continuous
D24V31, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   14 19
  12Q GAIN WILD-TYPE 35 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     14   19
  12Q GAIN WILD-TYPE   35   98
                                          clus
vv                                         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   14                 35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               19                 98
[1] 2 2
[1] FALSE
D24V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12Q GAIN MUTATED              1           9         12
  12Q GAIN WILD-TYPE           14          45         73
D24V33, multiclass
              clus
vv             12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 9                 45
  NEVER USED                 12                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V34, continuous
D24V35, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   15  4
  12Q GAIN WILD-TYPE 77 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     15    4
  12Q GAIN WILD-TYPE   77   14
         clus
vv        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ABSENT                15                 77
  PRESENT                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  12Q GAIN MUTATED             0        21     0
  12Q GAIN WILD-TYPE           5        79     2
D24V36, multiclass
             clus
vv            12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 21                 79
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V37, continuous
D24V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  12Q GAIN MUTATED         0        0         0         0        4        12
  12Q GAIN WILD-TYPE       5        1         1         1       30        65
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  12Q GAIN MUTATED           6        1         3          2          0
  12Q GAIN WILD-TYPE        31        3         5          3          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  12Q GAIN MUTATED           9         0          1         10         1
  12Q GAIN WILD-TYPE        35         1          2         32         6
                    vv
clus                 STAGE IVB
  12Q GAIN MUTATED           0
  12Q GAIN WILD-TYPE        12
D24V39, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  4                 30
  STAGE IB1                12                 65
  STAGE IB2                 6                 31
  STAGE II                  1                  3
  STAGE IIA                 3                  5
  STAGE IIA1                2                  3
  STAGE IIA2                0                  7
  STAGE IIB                 9                 35
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB               10                 32
  STAGE IVA                 1                  6
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    15   8
  13Q GAIN WILD-TYPE 196  59
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                23                255 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                 59 
$`13Q GAIN MUTATED`
TCGA-4J-AA1J TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7X8 
       17.82        35.01         0.46       100.14        17.85         2.73 
TCGA-C5-A8YR TCGA-DG-A2KH TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A5O9 TCGA-EA-A5ZF 
       27.52         1.12        31.36        13.05        25.91        27.22 
TCGA-EA-A97N TCGA-EK-A2PG TCGA-EX-A8YF TCGA-FU-A40J TCGA-MY-A5BE TCGA-PN-A8MA 
        0.36         1.51        15.55        14.01        35.05         2.96 
TCGA-Q1-A73R TCGA-VS-A8Q8 TCGA-VS-A8QH TCGA-VS-A9UA TCGA-VS-A9V4 
       18.64        32.15        39.78        28.50         4.34 

$`13Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML 
       57.73        53.16        38.99        35.61         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       40.93         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL 
       78.35        38.43        33.24        52.01        18.02        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      210.67       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      147.35        17.19       155.77       131.11        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61        50.99        45.83         8.35       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK 
       23.51        20.81        20.91        14.73        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       69.96        95.67        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        36.89        26.40        24.56        31.73        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
        0.30        24.82         7.46        14.89        26.79        27.29 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       27.25        24.00        13.48        12.59        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64        19.27         0.39         0.43         0.59         0.36 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK 
        1.45         0.13        40.96         4.31         0.10         0.43 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN 
       47.77         0.53         0.10         0.49         0.76         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92        15.22        14.70        19.79         8.32 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
       20.98        26.14         1.48        16.14        28.31        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       10.55         1.12        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       20.91        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
       13.35        22.52        19.56        17.82        19.56         8.35 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84        17.23        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73S 
       16.14        17.56        14.07        15.88         9.34        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59        14.60        11.67        93.99        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       10.03        46.52        45.57        32.42        23.97        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       65.49        53.59        36.13        11.51        59.18        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       40.87        16.64         4.73        33.37        40.14        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       15.68        56.35        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       43.40        48.39        29.95        27.12        24.30        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       45.11         1.71        14.53        27.25        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       41.52        26.07        15.85        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 
       67.20        18.84         5.16        18.25        17.75        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.36               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            100.14             210.67 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             17.85              23.67 
[1] "0.4 - 100.1 (17.9)" "0.0 - 210.7 (23.7)"
[1] "hr=" "2.3"
D25V2, continuous
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED    12   4   2   1
  13Q GAIN WILD-TYPE 123  66  19   7
D25V3, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               12                123
  T2                4                 66
  T3                2                 19
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    12   4
  13Q GAIN WILD-TYPE 117  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     12    4
  13Q GAIN WILD-TYPE  117   52
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               12                117
  1                4                 52
[1] 2 2
[1] FALSE
D25V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   12  0
  13Q GAIN WILD-TYPE 96 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     12    0
  13Q GAIN WILD-TYPE   96   10
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               12                 96
  1                0                 10
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     5  10
  13Q GAIN WILD-TYPE  50 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   10
  13Q GAIN WILD-TYPE   50  113
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 5                 50
  YES               10                113
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED               1                               15
  13Q GAIN WILD-TYPE             5                              227
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  13Q GAIN MUTATED                                               0
  13Q GAIN WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  13Q GAIN MUTATED                                     4
  13Q GAIN WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  13Q GAIN MUTATED                                           0
  13Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  13Q GAIN MUTATED                                              4
  13Q GAIN WILD-TYPE                                           13
D25V7, multiclass
                                               clus
vv                                              13Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            15
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 4
                                               clus
vv                                              13Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             227
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, continuous
D25V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     1
  13Q GAIN WILD-TYPE                                8    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED                           3
  13Q GAIN WILD-TYPE                        25
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           0    19
  13Q GAIN WILD-TYPE                                         2   183
D25V10, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                3                 25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   19                183
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  15
  13Q GAIN WILD-TYPE  23 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   15
  13Q GAIN WILD-TYPE   23  147
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 23
  NOT HISPANIC OR LATINO               15                147
[1] 2 2
[1] FALSE
D25V12, continuous
D25V13, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    11   9
  13Q GAIN WILD-TYPE 172  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     11    9
  13Q GAIN WILD-TYPE  172   65
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  TUMOR FREE               11                172
  WITH TUMOR                9                 65
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  13Q GAIN MUTATED     1  10  11   0   2
  13Q GAIN WILD-TYPE  17 119 104   1  22
D25V14, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  G1                1                 17
  G2               10                119
  G3               11                104
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V15, continuous
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 42 
        TCGA-2W-A8YY         TCGA-BI-A0VR         TCGA-C5-A1BJ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BQ         TCGA-C5-A1ME 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A2M2 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A7CM         TCGA-C5-A7CO 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-C5-A8XH         TCGA-C5-A907         TCGA-DG-A2KK 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-EK-A2RA         TCGA-EX-A69M 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3TX         TCGA-FU-A3WB 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-HM-A4S6         TCGA-IR-A3L7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JX-A3Q0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-MA-AA43         TCGA-MU-A5YI         TCGA-MU-A8JM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-Q1-A73S         TCGA-RA-A741 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-VS-A8QF         TCGA-VS-A94Z         TCGA-VS-A9V0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-WL-A834         TCGA-ZJ-A8QR         TCGA-ZJ-AAX4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ZJ-AAXA         TCGA-ZJ-AAXT         TCGA-ZJ-AB0I 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D25V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  13Q GAIN MUTATED                                             2
  13Q GAIN WILD-TYPE                                          36
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  13Q GAIN MUTATED                                        0
  13Q GAIN WILD-TYPE                                      9
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  13Q GAIN MUTATED                                                 0
  13Q GAIN WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  13Q GAIN MUTATED                3                  16
  13Q GAIN WILD-TYPE             59                 127
D25V17, multiclass
                                                 clus
vv                                                13Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 3
  LIFELONG NON-SMOKER                                           16
                                                 clus
vv                                                13Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  59
  LIFELONG NON-SMOKER                                            127
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V18, continuous
D25V19, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2  0
  13Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    0
  13Q GAIN WILD-TYPE   23    3
                         clus
vv                        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   2                 23
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D25V20, continuous
D25V21, continuous
D25V22, continuous
D25V23, continuous
D25V24, continuous
D25V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  13Q GAIN MUTATED                                     0
  13Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  13Q GAIN MUTATED                                     0
  13Q GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  13Q GAIN MUTATED                         3                       0
  13Q GAIN WILD-TYPE                      33                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  13Q GAIN MUTATED                         0
  13Q GAIN WILD-TYPE                       8
D25V26, multiclass
                                     clus
vv                                    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            3                 33
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  13Q GAIN MUTATED                                               0
  13Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  13Q GAIN MUTATED                                                1
  13Q GAIN WILD-TYPE                                             24
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  13Q GAIN MUTATED                                                                                   9
  13Q GAIN WILD-TYPE                                                                                73
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  13Q GAIN MUTATED                                                                                             11
  13Q GAIN WILD-TYPE                                                                                          110
D25V27, multiclass
                                                                                              clus
vv                                                                                             13Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               11
                                                                                              clus
vv                                                                                             13Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            73
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V28, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    7  8
  13Q GAIN WILD-TYPE 64 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7    8
  13Q GAIN WILD-TYPE   64   66
         clus
vv        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ABSENT                 7                 64
  PRESENT                8                 66
[1] 2 2
[1] FALSE
D25V29, continuous
D25V30, continuous
D25V31, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     2   9
  13Q GAIN WILD-TYPE  47 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    9
  13Q GAIN WILD-TYPE   47  108
                                          clus
vv                                         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    2                 47
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                9                108
[1] 2 2
[1] FALSE
D25V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  13Q GAIN MUTATED              0           5          5
  13Q GAIN WILD-TYPE           15          49         80
D25V33, multiclass
              clus
vv             13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CURRENT USER                0                 15
  FORMER USER                 5                 49
  NEVER USED                  5                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V34, continuous
D25V35, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    9  0
  13Q GAIN WILD-TYPE 83 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      9    0
  13Q GAIN WILD-TYPE   83   18
         clus
vv        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ABSENT                 9                 83
  PRESENT                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  13Q GAIN MUTATED             0         5     1
  13Q GAIN WILD-TYPE           5        95     1
D25V36, multiclass
             clus
vv            13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                  5                 95
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V37, continuous
D25V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  13Q GAIN MUTATED         1        0         0         0        3         8
  13Q GAIN WILD-TYPE       4        1         1         1       31        69
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  13Q GAIN MUTATED           5        0         0          0          0
  13Q GAIN WILD-TYPE        32        4         8          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  13Q GAIN MUTATED           1         0          1          3         1
  13Q GAIN WILD-TYPE        43         1          2         39         6
                    vv
clus                 STAGE IVB
  13Q GAIN MUTATED           0
  13Q GAIN WILD-TYPE        12
D25V39, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  3                 31
  STAGE IB1                 8                 69
  STAGE IB2                 5                 32
  STAGE II                  0                  4
  STAGE IIA                 0                  8
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 1                 43
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                3                 39
  STAGE IVA                 1                  6
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    36  10
  14Q GAIN WILD-TYPE 175  57
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                46                232 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                10                 57 
$`14Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BL TCGA-C5-A1M6 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A2LT 
       57.04       173.29        31.40        38.99        35.61        73.18 
TCGA-C5-A2LV TCGA-C5-A7CH TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-DS-A7WI TCGA-EA-A1QS 
       73.45       154.32         2.73        45.83         8.28        39.55 
TCGA-EA-A3QE TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N 
       25.02        31.73        14.89        25.91        27.22         0.36 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2R7 TCGA-EX-A3L1 TCGA-FU-A3HY TCGA-FU-A3NI 
        6.64        19.27         0.36        15.22        31.36        20.98 
TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3X TCGA-MA-AA43 
       28.37        44.61         0.30         0.82        19.56        11.38 
TCGA-MY-A5BD TCGA-MY-A913 TCGA-Q1-A6DT TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       54.81        17.23         9.04        32.42        23.97        19.96 
TCGA-VS-A953 TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UP 
       15.68        50.47        24.30        46.92        45.11        47.47 
TCGA-VS-A9UU TCGA-XS-A8TJ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       14.53        29.26         0.69         1.41 

$`14Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN 
       18.74        36.56       144.16       177.04        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       19.86        67.46        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ 
       52.01        18.02        17.85        20.42       210.67       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI 
      131.11        94.95         9.34        13.61        50.99         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
      146.86        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       14.73         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76        55.63        69.96        95.67 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HQ 
       22.98        16.83        16.18        17.52        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
       30.90        31.53        31.36        13.05        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       24.56        26.01         0.30        24.82         7.46        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       27.29        27.25        24.00        13.48        12.59        60.72 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R8 
       26.27         1.51         0.39         0.43         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL 
        0.13        40.96         4.31         0.10         0.43        47.77 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
        0.53         0.10         0.49         0.76         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
        7.92        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
       23.84        19.04        16.11        36.26        26.14         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       17.75        25.41        16.57        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        21.44        20.48        15.58         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        20.91        11.28         0.89        12.49 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       13.35        22.52        17.82        19.56         8.35         8.52 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       28.08        34.62        19.96        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        69.50        10.03        46.52 
TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       45.57        65.49        32.15        53.59        36.13        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       59.18        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       33.37        40.14        58.45        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       51.32        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR 
        1.71        14.53        27.25        47.87        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       15.85         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
       18.25        17.75         4.34        16.24        15.42        26.01 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         0.16         3.91 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.30               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            173.29             210.67 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            25.465             22.095 
[1] "0.3 - 173.3 (25.5)" "0.0 - 210.7 (22.1)"
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED    20  12   6   2
  14Q GAIN WILD-TYPE 115  58  15   6
D26V3, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               20                115
  T2               12                 58
  T3                6                 15
  T4                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    18   9
  14Q GAIN WILD-TYPE 111  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     18    9
  14Q GAIN WILD-TYPE  111   47
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               18                111
  1                9                 47
[1] 2 2
[1] FALSE
D26V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   20  2
  14Q GAIN WILD-TYPE 88  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     20    2
  14Q GAIN WILD-TYPE   88    8
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               20                 88
  1                2                  8
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     9  19
  14Q GAIN WILD-TYPE  46 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      9   19
  14Q GAIN WILD-TYPE   46  104
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 9                 46
  YES               19                104
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED               0                               41
  14Q GAIN WILD-TYPE             6                              201
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  14Q GAIN MUTATED                                               1
  14Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  14Q GAIN MUTATED                                     2
  14Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  14Q GAIN MUTATED                                           1
  14Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  14Q GAIN MUTATED                                              2
  14Q GAIN WILD-TYPE                                           15
D26V7, multiclass
                                               clus
vv                                              14Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            41
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              14Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             201
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, continuous
D26V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     5
  14Q GAIN WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED                           5
  14Q GAIN WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           0    32
  14Q GAIN WILD-TYPE                                         2   170
D26V10, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                                5                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   32                170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5  28
  14Q GAIN WILD-TYPE  18 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   28
  14Q GAIN WILD-TYPE   18  134
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 18
  NOT HISPANIC OR LATINO               28                134
[1] 2 2
[1] FALSE
D26V12, continuous
D26V13, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    32  10
  14Q GAIN WILD-TYPE 151  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     32   10
  14Q GAIN WILD-TYPE  151   64
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  TUMOR FREE               32                151
  WITH TUMOR               10                 64
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  14Q GAIN MUTATED     2  19  19   0   6
  14Q GAIN WILD-TYPE  16 110  96   1  18
D26V14, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  G1                2                 16
  G2               19                110
  G3               19                 96
  G4                0                  1
  GX                6                 18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V15, continuous
D26V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  14Q GAIN MUTATED                                             4
  14Q GAIN WILD-TYPE                                          34
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  14Q GAIN MUTATED                                        2
  14Q GAIN WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  14Q GAIN MUTATED                                                 2
  14Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  14Q GAIN MUTATED               12                  23
  14Q GAIN WILD-TYPE             50                 120
D26V17, multiclass
                                                 clus
vv                                                14Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                2
  CURRENT SMOKER                                                12
  LIFELONG NON-SMOKER                                           23
                                                 clus
vv                                                14Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     34
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  50
  LIFELONG NON-SMOKER                                            120
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V18, continuous
D26V19, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    5  0
  14Q GAIN WILD-TYPE 20  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5    0
  14Q GAIN WILD-TYPE   20    3
                         clus
vv                        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   5                 20
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D26V20, continuous
D26V21, continuous
D26V22, continuous
D26V23, continuous
D26V24, continuous
D26V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  14Q GAIN MUTATED                                     0
  14Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  14Q GAIN MUTATED                                     0
  14Q GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  14Q GAIN MUTATED                         5                       0
  14Q GAIN WILD-TYPE                      31                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  14Q GAIN MUTATED                         1
  14Q GAIN WILD-TYPE                       7
D26V26, multiclass
                                     clus
vv                                    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            5                 31
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  14Q GAIN MUTATED                                               0
  14Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  14Q GAIN MUTATED                                                6
  14Q GAIN WILD-TYPE                                             19
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  14Q GAIN MUTATED                                                                                  10
  14Q GAIN WILD-TYPE                                                                                72
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  14Q GAIN MUTATED                                                                                             22
  14Q GAIN WILD-TYPE                                                                                           99
D26V27, multiclass
                                                                                              clus
vv                                                                                             14Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               22
                                                                                              clus
vv                                                                                             14Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            72
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V28, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   11 12
  14Q GAIN WILD-TYPE 60 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     11   12
  14Q GAIN WILD-TYPE   60   62
         clus
vv        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ABSENT                11                 60
  PRESENT               12                 62
[1] 2 2
[1] FALSE
D26V29, continuous
D26V30, continuous
D26V31, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    6 21
  14Q GAIN WILD-TYPE 43 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6   21
  14Q GAIN WILD-TYPE   43   96
                                          clus
vv                                         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               21                 96
[1] 2 2
[1] FALSE
D26V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  14Q GAIN MUTATED              4           5         21
  14Q GAIN WILD-TYPE           11          49         64
D26V33, multiclass
              clus
vv             14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CURRENT USER                4                 11
  FORMER USER                 5                 49
  NEVER USED                 21                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V34, continuous
D26V35, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   15  2
  14Q GAIN WILD-TYPE 77 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15    2
  14Q GAIN WILD-TYPE   77   16
         clus
vv        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ABSENT                15                 77
  PRESENT                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  14Q GAIN MUTATED             0        18     0
  14Q GAIN WILD-TYPE           5        82     2
D26V36, multiclass
             clus
vv            14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 18                 82
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V37, continuous
D26V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  14Q GAIN MUTATED         1        0         0         0        6        12
  14Q GAIN WILD-TYPE       4        1         1         1       28        65
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  14Q GAIN MUTATED           4        1         2          2          1
  14Q GAIN WILD-TYPE        33        3         6          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  14Q GAIN MUTATED           8         0          1          7         2
  14Q GAIN WILD-TYPE        36         1          2         35         5
                    vv
clus                 STAGE IVB
  14Q GAIN MUTATED           0
  14Q GAIN WILD-TYPE        12
D26V39, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  6                 28
  STAGE IB1                12                 65
  STAGE IB2                 4                 33
  STAGE II                  1                  3
  STAGE IIA                 2                  6
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                 8                 36
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                7                 35
  STAGE IVA                 2                  5
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    39  10
  15Q GAIN WILD-TYPE 172  57
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                49                229 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 57 
$`15Q GAIN MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1ME 
       17.82        49.48        18.74        31.40        30.21        57.73 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LZ 
       35.61         2.43        40.93         3.58        73.18       100.14 
TCGA-C5-A3HE TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8ZZ 
       18.02       101.82        20.35         9.34         2.73        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KL TCGA-EA-A3HQ TCGA-EA-A5O9 TCGA-EK-A2RC 
       14.73         1.12        44.94        37.35        25.91         4.31 
TCGA-EK-A2RD TCGA-EK-A3GM TCGA-EX-A3L1 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23L 
        0.10         0.76        15.22        19.79        15.55        23.84 
TCGA-HG-A9SC TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A5U2 
       16.57        27.42        21.44        20.91        11.28         0.30 
TCGA-MA-AA43 TCGA-MY-A5BE TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EC 
       11.38        35.05        22.62        19.59        12.16        46.52 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A9UB TCGA-VS-A9UC 
       32.42        23.97        11.51        59.18        29.95        27.12 
TCGA-VS-A9UU 
       14.53 

$`15Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       17.52        57.04        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ 
       67.46        46.32        35.01        53.16        38.99         0.46 
TCGA-C5-A1ML TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 
       20.91        44.22        73.45        83.05        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       33.24        52.01        17.85        20.42       210.67       154.32 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      134.33        15.48       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       94.95        13.61        50.99        45.83         8.35       146.86 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-DG-A2KJ TCGA-DG-A2KK 
       99.91        23.51        27.52        20.81        95.11        82.06 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63        69.96 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       95.67        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        40.87        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        36.89        26.40        24.56        31.73        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
        0.30        24.82         7.46        14.89        26.79        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       27.25        27.22        24.00        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
       60.72        26.27         6.64         1.51        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.36         1.45         0.13        40.96 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        0.43        47.77         0.53         0.10         0.49         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG 
       20.35         7.92        14.70         8.32         1.22        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
       16.11        31.36        36.26        20.98        26.14         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       17.75        25.41        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK 
       81.96        29.85        36.36         3.29        24.56        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        28.37         8.28        18.15        21.11       209.59 
TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       44.61         0.89        12.49         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y 
       19.56        17.82        19.56         8.35         8.52        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
       34.62        19.96        54.81        20.84        17.23         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD 
       14.07        15.88         9.34        18.64        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL 
       93.99        69.50        10.03        45.57        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       32.15        53.59        36.13        39.78        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       16.64         4.73        33.37        40.14        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       56.35        55.50        50.14        51.32        50.47        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       48.39        28.50        24.30        46.92        45.11         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       14.53        27.25        47.87        47.47        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       15.85         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
       18.25        17.75         4.34        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       29.26        67.59        19.13         0.69         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.10               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            101.82             210.67 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             20.91              24.30 
[1] "0.1 - 101.8 (20.9)" "0.0 - 210.7 (24.3)"
[1] "hr=" "1"  
D27V2, continuous
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED    16  16   6   0
  15Q GAIN WILD-TYPE 119  54  15   8
D27V3, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               16                119
  T2               16                 54
  T3                6                 15
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    21  10
  15Q GAIN WILD-TYPE 108  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     21   10
  15Q GAIN WILD-TYPE  108   46
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               21                108
  1               10                 46
[1] 2 2
[1] FALSE
D27V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   22  0
  15Q GAIN WILD-TYPE 86 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     22    0
  15Q GAIN WILD-TYPE   86   10
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               22                 86
  1                0                 10
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6 25
  15Q GAIN WILD-TYPE 49 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6   25
  15Q GAIN WILD-TYPE   49   98
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 6                 49
  YES               25                 98
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED               3                               43
  15Q GAIN WILD-TYPE             3                              199
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  15Q GAIN MUTATED                                               3
  15Q GAIN WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  15Q GAIN MUTATED                                     2
  15Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  15Q GAIN MUTATED                                           0
  15Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  15Q GAIN MUTATED                                              1
  15Q GAIN WILD-TYPE                                           16
D27V7, multiclass
                                               clus
vv                                              15Q GAIN MUTATED
  ADENOSQUAMOUS                                                3
  CERVICAL SQUAMOUS CELL CARCINOMA                            43
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              15Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  3
  CERVICAL SQUAMOUS CELL CARCINOMA                             199
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, continuous
D27V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  3     3
  15Q GAIN WILD-TYPE                                5    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED                           2
  15Q GAIN WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           0    36
  15Q GAIN WILD-TYPE                                         2   166
D27V10, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  5
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                2                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   36                166
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     5  30
  15Q GAIN WILD-TYPE  18 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      5   30
  15Q GAIN WILD-TYPE   18  132
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 18
  NOT HISPANIC OR LATINO               30                132
[1] 2 2
[1] FALSE
D27V12, continuous
D27V13, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    34  11
  15Q GAIN WILD-TYPE 149  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     34   11
  15Q GAIN WILD-TYPE  149   63
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  TUMOR FREE               34                149
  WITH TUMOR               11                 63
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  15Q GAIN MUTATED     5  20  24   0   2
  15Q GAIN WILD-TYPE  13 109  91   1  22
D27V14, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  G1                5                 13
  G2               20                109
  G3               24                 91
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, continuous
D27V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  15Q GAIN MUTATED                                             8
  15Q GAIN WILD-TYPE                                          30
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  15Q GAIN MUTATED                                        0
  15Q GAIN WILD-TYPE                                      9
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  15Q GAIN MUTATED                                                 0
  15Q GAIN WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  15Q GAIN MUTATED               13                  26
  15Q GAIN WILD-TYPE             49                 117
D27V17, multiclass
                                                 clus
vv                                                15Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                13
  LIFELONG NON-SMOKER                                           26
                                                 clus
vv                                                15Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  49
  LIFELONG NON-SMOKER                                            117
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V18, continuous
D27V19, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6  1
  15Q GAIN WILD-TYPE 19  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6    1
  15Q GAIN WILD-TYPE   19    2
                         clus
vv                        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   6                 19
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D27V20, continuous
D27V21, continuous
D27V22, continuous
D27V23, continuous
D27V24, continuous
D27V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  15Q GAIN MUTATED                                     0
  15Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  15Q GAIN MUTATED                                     0
  15Q GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  15Q GAIN MUTATED                         7                       0
  15Q GAIN WILD-TYPE                      29                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  15Q GAIN MUTATED                         1
  15Q GAIN WILD-TYPE                       7
D27V26, multiclass
                                     clus
vv                                    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            7                 29
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  15Q GAIN MUTATED                                               1
  15Q GAIN WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  15Q GAIN MUTATED                                                7
  15Q GAIN WILD-TYPE                                             18
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  15Q GAIN MUTATED                                                                                  12
  15Q GAIN WILD-TYPE                                                                                70
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  15Q GAIN MUTATED                                                                                             21
  15Q GAIN WILD-TYPE                                                                                          100
D27V27, multiclass
                                                                                              clus
vv                                                                                             15Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               21
                                                                                              clus
vv                                                                                             15Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V28, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   12 14
  15Q GAIN WILD-TYPE 59 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     12   14
  15Q GAIN WILD-TYPE   59   60
         clus
vv        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ABSENT                12                 59
  PRESENT               14                 60
[1] 2 2
[1] FALSE
D27V29, continuous
D27V30, continuous
D27V31, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     9  17
  15Q GAIN WILD-TYPE  40 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9   17
  15Q GAIN WILD-TYPE   40  100
                                          clus
vv                                         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               17                100
[1] 2 2
[1] FALSE
D27V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  15Q GAIN MUTATED              3           6         15
  15Q GAIN WILD-TYPE           12          48         70
D27V33, multiclass
              clus
vv             15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CURRENT USER                3                 12
  FORMER USER                 6                 48
  NEVER USED                 15                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V34, continuous
D27V35, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   14  3
  15Q GAIN WILD-TYPE 78 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     14    3
  15Q GAIN WILD-TYPE   78   15
         clus
vv        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ABSENT                14                 78
  PRESENT                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  15Q GAIN MUTATED             1        23     0
  15Q GAIN WILD-TYPE           4        77     2
D27V36, multiclass
             clus
vv            15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 23                 77
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V37, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 15 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-GH-A9DA         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3Q8         TCGA-MA-AA3W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-MA-AA3Z         TCGA-MA-AA42         TCGA-MU-A51Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-MY-A913         TCGA-ZX-AA5X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D27V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  15Q GAIN MUTATED         0        0         0         0        4        12
  15Q GAIN WILD-TYPE       5        1         1         1       30        65
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  15Q GAIN MUTATED           7        1         4          2          0
  15Q GAIN WILD-TYPE        30        3         4          3          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  15Q GAIN MUTATED           9         0          0         12         1
  15Q GAIN WILD-TYPE        35         1          3         30         6
                    vv
clus                 STAGE IVB
  15Q GAIN MUTATED           0
  15Q GAIN WILD-TYPE        12
D27V39, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  4                 30
  STAGE IB1                12                 65
  STAGE IB2                 7                 30
  STAGE II                  1                  3
  STAGE IIA                 4                  4
  STAGE IIA1                2                  3
  STAGE IIA2                0                  7
  STAGE IIB                 9                 35
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB               12                 30
  STAGE IVA                 1                  6
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    31  11
  16P GAIN WILD-TYPE 180  56
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                42                236 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                11                 56 
$`16P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A2LS 
       57.04        31.40        46.32        38.99        35.61        44.22 
TCGA-C5-A7CH TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A3LQ 
      154.32         2.73        27.52         1.12        95.11        22.98 
TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF 
        8.28        37.35        13.05        31.73        25.91        27.22 
TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EX-A69L TCGA-FU-A23L 
        0.36        26.27         0.10        47.77        19.79        23.84 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-JW-A5VJ TCGA-JX-A3Q0 TCGA-MA-AA3X TCGA-PN-A8MA 
       20.98        14.01        21.44       209.59        19.56         2.96 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8QA TCGA-VS-A953 TCGA-VS-A9U5 TCGA-VS-A9U6 
       93.99        12.16        36.13        15.68        50.47        43.40 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UP TCGA-VS-A9UU TCGA-XS-A8TJ TCGA-ZJ-AAXA 
       46.92        45.11        47.47        14.53        29.26         1.41 

$`16P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
        5.46        19.86        67.46        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC 
      155.77       131.11        94.95         9.34        13.61        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT 
       45.83         8.35       146.86        99.91        23.51        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.91        14.73        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        36.76        55.63        69.96        95.67        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18        17.52        39.55        40.87        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       31.36        25.02        36.89        26.40        24.56        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
        0.30        24.82         7.46        14.89        26.79        27.29 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       27.25        24.00        13.48        12.59        60.72         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        1.51        19.27         0.39         0.43         0.59         0.36 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RK TCGA-EK-A2RN 
        1.45         0.13        40.96         4.31         0.43         0.53 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.49         0.76         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
       15.22        14.70         8.32        15.55         1.22        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       16.11        31.36        36.26        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       28.31        35.44        10.55         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       16.57        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       129.37        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK 
       29.85        36.36        27.42         3.29        24.56        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 
       15.58        28.37         8.28        18.15        21.11        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       20.91        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       13.35        22.52        17.82        19.56         8.35         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84        17.23        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB 
       22.62        19.59        14.60        11.67        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       46.52        45.57        32.42        23.97        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        53.59        11.51        59.18        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       40.87        16.64         4.73        33.37        40.14        58.45 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U7 TCGA-VS-A9UA 
       56.35        55.50        50.14        51.32        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       29.95        27.12        24.30         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY 
       47.87        41.52        26.07        15.85         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       67.20        18.84         5.16        18.25        17.75         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       16.24        15.42        26.01        67.59        19.13         0.69 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.10               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            209.59             210.67 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             27.37              21.01 
[1] "0.1 - 209.6 (27.4)" "0.0 - 210.7 (21.0)"
[1] "hr=" "1"  
D28V2, continuous
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED    19  13   5   3
  16P GAIN WILD-TYPE 116  57  16   5
D28V3, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               19                116
  T2               13                 57
  T3                5                 16
  T4                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    18  12
  16P GAIN WILD-TYPE 111  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     18   12
  16P GAIN WILD-TYPE  111   44
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               18                111
  1               12                 44
[1] 2 2
[1] FALSE
D28V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   21  1
  16P GAIN WILD-TYPE 87  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     21    1
  16P GAIN WILD-TYPE   87    9
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               21                 87
  1                1                  9
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     7  19
  16P GAIN WILD-TYPE  48 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      7   19
  16P GAIN WILD-TYPE   48  104
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 7                 48
  YES               19                104
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED               1                               38
  16P GAIN WILD-TYPE             5                              204
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16P GAIN MUTATED                                               1
  16P GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16P GAIN MUTATED                                     2
  16P GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16P GAIN MUTATED                                           0
  16P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16P GAIN MUTATED                                              2
  16P GAIN WILD-TYPE                                           15
D28V7, multiclass
                                               clus
vv                                              16P GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              16P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             204
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, continuous
D28V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  2     3
  16P GAIN WILD-TYPE                                6    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED                           6
  16P GAIN WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           0    23
  16P GAIN WILD-TYPE                                         2   179
D28V10, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                6                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   23                179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     2  24
  16P GAIN WILD-TYPE  21 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   24
  16P GAIN WILD-TYPE   21  138
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 21
  NOT HISPANIC OR LATINO               24                138
[1] 2 2
[1] FALSE
D28V12, continuous
D28V13, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    25  12
  16P GAIN WILD-TYPE 158  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     25   12
  16P GAIN WILD-TYPE  158   62
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  TUMOR FREE               25                158
  WITH TUMOR               12                 62
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  16P GAIN MUTATED     3  18  17   0   6
  16P GAIN WILD-TYPE  15 111  98   1  18
D28V14, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  G1                3                 15
  G2               18                111
  G3               17                 98
  G4                0                  1
  GX                6                 18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, continuous
D28V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16P GAIN MUTATED                                             2
  16P GAIN WILD-TYPE                                          36
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  16P GAIN MUTATED                                        3
  16P GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  16P GAIN MUTATED                                                 1
  16P GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16P GAIN MUTATED               11                  20
  16P GAIN WILD-TYPE             51                 123
D28V17, multiclass
                                                 clus
vv                                                16P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                11
  LIFELONG NON-SMOKER                                           20
                                                 clus
vv                                                16P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  51
  LIFELONG NON-SMOKER                                            123
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V18, continuous
D28V19, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  0
  16P GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    0
  16P GAIN WILD-TYPE   21    3
                         clus
vv                        16P GAIN MUTATED 16P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D28V20, continuous
D28V21, continuous
D28V22, continuous
D28V23, continuous
D28V24, continuous
D28V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  16P GAIN MUTATED                                     0
  16P GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  16P GAIN MUTATED                                     0
  16P GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  16P GAIN MUTATED                         5                       0
  16P GAIN WILD-TYPE                      31                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16P GAIN MUTATED                         1
  16P GAIN WILD-TYPE                       7
D28V26, multiclass
                                     clus
vv                                    16P GAIN MUTATED 16P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            5                 31
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  16P GAIN MUTATED                                               0
  16P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  16P GAIN MUTATED                                                5
  16P GAIN WILD-TYPE                                             20
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16P GAIN MUTATED                                                                                  11
  16P GAIN WILD-TYPE                                                                                71
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16P GAIN MUTATED                                                                                             18
  16P GAIN WILD-TYPE                                                                                          103
D28V27, multiclass
                                                                                              clus
vv                                                                                             16P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               18
                                                                                              clus
vv                                                                                             16P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            71
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V28, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   11 11
  16P GAIN WILD-TYPE 60 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     11   11
  16P GAIN WILD-TYPE   60   63
         clus
vv        16P GAIN MUTATED 16P GAIN WILD-TYPE
  ABSENT                11                 60
  PRESENT               11                 63
[1] 2 2
[1] FALSE
D28V29, continuous
D28V30, continuous
D28V31, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    5 23
  16P GAIN WILD-TYPE 44 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5   23
  16P GAIN WILD-TYPE   44   94
                                          clus
vv                                         16P GAIN MUTATED 16P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    5                 44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               23                 94
[1] 2 2
[1] FALSE
D28V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16P GAIN MUTATED              1           6         14
  16P GAIN WILD-TYPE           14          48         71
D28V33, multiclass
              clus
vv             16P GAIN MUTATED 16P GAIN WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 6                 48
  NEVER USED                 14                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V34, continuous
D28V35, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   10  4
  16P GAIN WILD-TYPE 82 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     10    4
  16P GAIN WILD-TYPE   82   14
         clus
vv        16P GAIN MUTATED 16P GAIN WILD-TYPE
  ABSENT                10                 82
  PRESENT                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  16P GAIN MUTATED             0        16     1
  16P GAIN WILD-TYPE           5        84     1
D28V36, multiclass
             clus
vv            16P GAIN MUTATED 16P GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 16                 84
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V37, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1ML         TCGA-C5-A1MN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MA-AA3W         TCGA-MA-AA3Z         TCGA-MA-AA42 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ZX-AA5X 
"16P GAIN WILD-TYPE" 
D28V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  16P GAIN MUTATED         0        0         0         0        4        11
  16P GAIN WILD-TYPE       5        1         1         1       30        66
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  16P GAIN MUTATED           4        1         1          2          1
  16P GAIN WILD-TYPE        33        3         7          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  16P GAIN MUTATED           8         1          0          8         2
  16P GAIN WILD-TYPE        36         0          3         34         5
                    vv
clus                 STAGE IVB
  16P GAIN MUTATED           1
  16P GAIN WILD-TYPE        11
D28V39, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  4                 30
  STAGE IB1                11                 66
  STAGE IB2                 4                 33
  STAGE II                  1                  3
  STAGE IIA                 1                  7
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                 8                 36
  STAGE III                 1                  0
  STAGE IIIA                0                  3
  STAGE IIIB                8                 34
  STAGE IVA                 2                  5
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    27  10
  16Q GAIN WILD-TYPE 184  57
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                37                241 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                 57 
$`16Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A7CH 
       57.04        31.40        46.32        38.99        35.61       154.32 
TCGA-C5-A7UC TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A3LQ 
       17.19         2.73        27.52         1.12        95.11        22.98 
TCGA-DS-A7WI TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2H1 
        8.28        13.05        31.73        27.22         0.36        26.27 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A40J TCGA-JW-A5VJ TCGA-JX-A3Q0 
       15.22        19.79        23.84        14.01        21.44       209.59 
TCGA-MA-AA3X TCGA-PN-A8MA TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8QA TCGA-VS-A950 
       19.56         2.96        11.67        12.16        36.13        40.14 
TCGA-VS-A953 TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UP TCGA-VS-A9UU TCGA-XS-A8TJ 
       15.68        46.92        45.11        47.47        14.53        29.26 
TCGA-ZJ-AAXA 
        1.41 

$`16Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
        5.46        19.86        67.46        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      210.67       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC 
      155.77       131.11        94.95         9.34        13.61        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT 
       45.83         8.35       146.86        99.91        23.51        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
       20.91        14.73        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        36.76        55.63        69.96        95.67        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18        17.52        39.55        40.87        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.53        31.36        25.02        36.89        26.40        24.56 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       25.91        27.29        27.25        24.00        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL 
       60.72         6.64         1.51        19.27         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC 
        0.59         0.36         1.45         0.13        40.96         4.31 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.10         0.43        47.77         0.53         0.10         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M 
        0.76         0.03        20.35         7.92        14.70         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       15.55         1.22        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
       20.98        26.14         1.48        16.14        28.31        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       10.55         1.12        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        8.28        18.15        21.11        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
        0.89        12.49         0.30         0.82        13.35        22.52 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         8.35         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       34.62        19.96        54.81        35.05        20.84        17.23 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       14.60        93.99        69.50        10.03        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       32.42        23.97        19.96        65.49        32.15        53.59 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       11.51        59.18        39.78        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
        4.73        33.37        58.45        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       51.32        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       27.12        24.30         1.71        14.53        27.25        47.87 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.52        26.07        15.85         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.84         5.16        18.25        17.75         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
       15.42        26.01        67.59        19.13         0.69         0.16 
TCGA-ZX-AA5X 
        3.91 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.36               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            209.59             210.67 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             23.84              22.62 
[1] "0.4 - 209.6 (23.8)" "0.0 - 210.7 (22.6)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED    15  12   6   2
  16Q GAIN WILD-TYPE 120  58  15   6
D29V3, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               15                120
  T2               12                 58
  T3                6                 15
  T4                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    17   9
  16Q GAIN WILD-TYPE 112  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     17    9
  16Q GAIN WILD-TYPE  112   47
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               17                112
  1                9                 47
[1] 2 2
[1] FALSE
D29V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   20  0
  16Q GAIN WILD-TYPE 88 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     20    0
  16Q GAIN WILD-TYPE   88   10
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               20                 88
  1                0                 10
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     7  18
  16Q GAIN WILD-TYPE  48 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      7   18
  16Q GAIN WILD-TYPE   48  105
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 7                 48
  YES               18                105
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED               1                               36
  16Q GAIN WILD-TYPE             5                              206
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16Q GAIN MUTATED                                               0
  16Q GAIN WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16Q GAIN MUTATED                                     1
  16Q GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16Q GAIN MUTATED                                           0
  16Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16Q GAIN MUTATED                                              2
  16Q GAIN WILD-TYPE                                           15
D29V7, multiclass
                                               clus
vv                                              16Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            36
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              16Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             206
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, continuous
D29V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  2     3
  16Q GAIN WILD-TYPE                                6    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED                           5
  16Q GAIN WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           0    20
  16Q GAIN WILD-TYPE                                         2   182
D29V10, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                5                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   20                182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2  20
  16Q GAIN WILD-TYPE  21 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   20
  16Q GAIN WILD-TYPE   21  142
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 21
  NOT HISPANIC OR LATINO               20                142
[1] 2 2
[1] FALSE
D29V12, continuous
D29V13, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    22  13
  16Q GAIN WILD-TYPE 161  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     22   13
  16Q GAIN WILD-TYPE  161   61
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  TUMOR FREE               22                161
  WITH TUMOR               13                 61
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  16Q GAIN MUTATED     2  13  20   0   5
  16Q GAIN WILD-TYPE  16 116  95   1  19
D29V14, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  G1                2                 16
  G2               13                116
  G3               20                 95
  G4                0                  1
  GX                5                 19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, continuous
D29V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16Q GAIN MUTATED                                             2
  16Q GAIN WILD-TYPE                                          36
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  16Q GAIN MUTATED                                        3
  16Q GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  16Q GAIN MUTATED                                                 1
  16Q GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16Q GAIN MUTATED                9                  18
  16Q GAIN WILD-TYPE             53                 125
D29V17, multiclass
                                                 clus
vv                                                16Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 9
  LIFELONG NON-SMOKER                                           18
                                                 clus
vv                                                16Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  53
  LIFELONG NON-SMOKER                                            125
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V18, continuous
D29V19, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    4  0
  16Q GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    0
  16Q GAIN WILD-TYPE   21    3
                         clus
vv                        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D29V20, continuous
D29V21, continuous
D29V22, continuous
D29V23, continuous
D29V24, continuous
D29V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  16Q GAIN MUTATED                                     0
  16Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  16Q GAIN MUTATED                                     0
  16Q GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  16Q GAIN MUTATED                         6                       0
  16Q GAIN WILD-TYPE                      30                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16Q GAIN MUTATED                         1
  16Q GAIN WILD-TYPE                       7
D29V26, multiclass
                                     clus
vv                                    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            6                 30
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  16Q GAIN MUTATED                                               0
  16Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  16Q GAIN MUTATED                                                4
  16Q GAIN WILD-TYPE                                             21
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16Q GAIN MUTATED                                                                                   9
  16Q GAIN WILD-TYPE                                                                                73
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16Q GAIN MUTATED                                                                                             17
  16Q GAIN WILD-TYPE                                                                                          104
D29V27, multiclass
                                                                                              clus
vv                                                                                             16Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               17
                                                                                              clus
vv                                                                                             16Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            73
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V28, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    8 11
  16Q GAIN WILD-TYPE 63 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      8   11
  16Q GAIN WILD-TYPE   63   63
         clus
vv        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ABSENT                 8                 63
  PRESENT               11                 63
[1] 2 2
[1] FALSE
D29V29, continuous
D29V30, continuous
D29V31, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    5 21
  16Q GAIN WILD-TYPE 44 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5   21
  16Q GAIN WILD-TYPE   44   96
                                          clus
vv                                         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    5                 44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               21                 96
[1] 2 2
[1] FALSE
D29V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16Q GAIN MUTATED              2           7         11
  16Q GAIN WILD-TYPE           13          47         74
D29V33, multiclass
              clus
vv             16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CURRENT USER                2                 13
  FORMER USER                 7                 47
  NEVER USED                 11                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V34, continuous
D29V35, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    9  2
  16Q GAIN WILD-TYPE 83 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      9    2
  16Q GAIN WILD-TYPE   83   16
         clus
vv        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ABSENT                 9                 83
  PRESENT                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  16Q GAIN MUTATED             0        14     1
  16Q GAIN WILD-TYPE           5        86     1
D29V36, multiclass
             clus
vv            16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 14                 86
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V37, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1ML         TCGA-C5-A1MN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MA-AA3W         TCGA-MA-AA3Z         TCGA-MA-AA42 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ZX-AA5X 
"16Q GAIN WILD-TYPE" 
D29V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  16Q GAIN MUTATED         0        0         0         0        6         8
  16Q GAIN WILD-TYPE       5        1         1         1       28        69
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  16Q GAIN MUTATED           2        0         1          3          1
  16Q GAIN WILD-TYPE        35        4         7          2          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  16Q GAIN MUTATED           7         1          1          8         2
  16Q GAIN WILD-TYPE        37         0          2         34         5
                    vv
clus                 STAGE IVB
  16Q GAIN MUTATED           0
  16Q GAIN WILD-TYPE        12
D29V39, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  6                 28
  STAGE IB1                 8                 69
  STAGE IB2                 2                 35
  STAGE II                  0                  4
  STAGE IIA                 1                  7
  STAGE IIA1                3                  2
  STAGE IIA2                1                  6
  STAGE IIB                 7                 37
  STAGE III                 1                  0
  STAGE IIIA                1                  2
  STAGE IIIB                8                 34
  STAGE IVA                 2                  5
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    15   7
  17P GAIN WILD-TYPE 196  60
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                256 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                 60 
$`17P GAIN MUTATED`
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A7CH TCGA-C5-A7UE 
       23.67        31.40        35.01        35.61       154.32       155.77 
TCGA-DG-A2KH TCGA-DS-A3LQ TCGA-EA-A3HR TCGA-EK-A2PM TCGA-FU-A40J TCGA-JX-A5QV 
        1.12        22.98        30.90         0.59        14.01        20.91 
TCGA-MA-AA43 TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EJ 
       11.38        17.23        15.95        93.99        46.52        19.96 
TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9V4 
       50.47        24.30        14.53         4.34 

$`17P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
        5.46        19.86        67.46        46.32        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       53.16        38.99         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       210.67       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
      147.35        17.19       131.11        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ 
       23.51        27.52        20.81        20.91        14.73        95.11 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       55.63        69.96        95.67        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28        39.55        40.87        37.35        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
        0.36        12.59        60.72        26.27         6.64         1.51 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       19.27         0.39         0.43         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
       40.96         4.31         0.10         0.43        47.77         0.53 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.49         0.76         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       15.22        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
       26.14         1.48        16.14        28.31        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12        17.75        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU 
        8.28        18.15        21.11       209.59        44.61        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
        0.89        12.49         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y 
       19.56        17.82        19.56         8.35         8.52        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH 
       11.67        12.16        69.50        10.03        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       23.97        65.49        32.15        53.59        36.13        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       59.18        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       33.37        40.14        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       50.14        51.32        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO 
       27.12        46.92        45.11         1.71        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.59               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            155.77             210.67 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            23.325             23.065 
[1] "0.6 - 155.8 (23.3)" "0.0 - 210.7 (23.1)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED     5   4   6   1
  17P GAIN WILD-TYPE 130  66  15   7
D30V3, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                5                130
  T2                4                 66
  T3                6                 15
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     5   5
  17P GAIN WILD-TYPE 124  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    5
  17P GAIN WILD-TYPE  124   51
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                5                124
  1                5                 51
[1] 2 2
[1] FALSE
D30V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    9  2
  17P GAIN WILD-TYPE 99  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9    2
  17P GAIN WILD-TYPE   99    8
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                9                 99
  1                2                  8
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     2  12
  17P GAIN WILD-TYPE  53 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2   12
  17P GAIN WILD-TYPE   53  111
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 2                 53
  YES               12                111
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED               1                               18
  17P GAIN WILD-TYPE             5                              224
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17P GAIN MUTATED                                               0
  17P GAIN WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17P GAIN MUTATED                                     2
  17P GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17P GAIN MUTATED                                           0
  17P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17P GAIN MUTATED                                              1
  17P GAIN WILD-TYPE                                           16
D30V7, multiclass
                                               clus
vv                                              17P GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            18
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              17P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             224
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, continuous
D30V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     0
  17P GAIN WILD-TYPE                                8    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED                           1
  17P GAIN WILD-TYPE                        27
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0    18
  17P GAIN WILD-TYPE                                         2   184
D30V10, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                1                 27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   18                184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     2   8
  17P GAIN WILD-TYPE  21 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    8
  17P GAIN WILD-TYPE   21  154
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 21
  NOT HISPANIC OR LATINO                8                154
[1] 2 2
[1] FALSE
D30V12, continuous
D30V13, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    13   7
  17P GAIN WILD-TYPE 170  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     13    7
  17P GAIN WILD-TYPE  170   67
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  TUMOR FREE               13                170
  WITH TUMOR                7                 67
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  17P GAIN MUTATED     0   9  12   0   1
  17P GAIN WILD-TYPE  18 120 103   1  23
D30V14, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  G1                0                 18
  G2                9                120
  G3               12                103
  G4                0                  1
  GX                1                 23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, continuous
D30V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17P GAIN MUTATED                                             3
  17P GAIN WILD-TYPE                                          35
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  17P GAIN MUTATED                                        1
  17P GAIN WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  17P GAIN MUTATED                                                 1
  17P GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17P GAIN MUTATED                3                  11
  17P GAIN WILD-TYPE             59                 132
D30V17, multiclass
                                                 clus
vv                                                17P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 3
  LIFELONG NON-SMOKER                                           11
                                                 clus
vv                                                17P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     35
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  59
  LIFELONG NON-SMOKER                                            132
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V18, continuous
D30V19, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    4  0
  17P GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    0
  17P GAIN WILD-TYPE   21    3
                         clus
vv                        17P GAIN MUTATED 17P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D30V20, continuous
D30V21, continuous
D30V22, continuous
D30V23, continuous
D30V24, continuous
D30V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  17P GAIN MUTATED                                     0
  17P GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  17P GAIN MUTATED                                     1
  17P GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  17P GAIN MUTATED                         2                       0
  17P GAIN WILD-TYPE                      34                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17P GAIN MUTATED                         0
  17P GAIN WILD-TYPE                       8
D30V26, multiclass
                                     clus
vv                                    17P GAIN MUTATED 17P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                            2                 34
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  17P GAIN MUTATED                                               0
  17P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  17P GAIN MUTATED                                                4
  17P GAIN WILD-TYPE                                             21
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17P GAIN MUTATED                                                                                   8
  17P GAIN WILD-TYPE                                                                                74
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17P GAIN MUTATED                                                                                              7
  17P GAIN WILD-TYPE                                                                                          114
D30V27, multiclass
                                                                                              clus
vv                                                                                             17P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                7
                                                                                              clus
vv                                                                                             17P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            74
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V28, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    3  6
  17P GAIN WILD-TYPE 68 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    6
  17P GAIN WILD-TYPE   68   68
         clus
vv        17P GAIN MUTATED 17P GAIN WILD-TYPE
  ABSENT                 3                 68
  PRESENT                6                 68
[1] 2 2
[1] FALSE
D30V29, continuous
D30V30, continuous
D30V31, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4   5
  17P GAIN WILD-TYPE  45 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    5
  17P GAIN WILD-TYPE   45  112
                                          clus
vv                                         17P GAIN MUTATED 17P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 45
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                5                112
[1] 2 2
[1] FALSE
D30V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17P GAIN MUTATED              0           5          6
  17P GAIN WILD-TYPE           15          49         79
D30V33, multiclass
              clus
vv             17P GAIN MUTATED 17P GAIN WILD-TYPE
  CURRENT USER                0                 15
  FORMER USER                 5                 49
  NEVER USED                  6                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V34, continuous
D30V35, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    6  2
  17P GAIN WILD-TYPE 86 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      6    2
  17P GAIN WILD-TYPE   86   16
         clus
vv        17P GAIN MUTATED 17P GAIN WILD-TYPE
  ABSENT                 6                 86
  PRESENT                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  17P GAIN MUTATED             0        11     0
  17P GAIN WILD-TYPE           5        89     2
D30V36, multiclass
             clus
vv            17P GAIN MUTATED 17P GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 11                 89
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V37, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A3JK         TCGA-JW-A852 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-MA-AA3W         TCGA-MA-AA3Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MA-AA42         TCGA-MU-A51Y         TCGA-MU-A8JM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ZX-AA5X 
"17P GAIN WILD-TYPE" 
D30V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  17P GAIN MUTATED         0        0         0         0        0         7
  17P GAIN WILD-TYPE       5        1         1         1       34        70
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  17P GAIN MUTATED           0        1         1          0          0
  17P GAIN WILD-TYPE        37        3         7          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  17P GAIN MUTATED           5         0          1          5         1
  17P GAIN WILD-TYPE        39         1          2         37         6
                    vv
clus                 STAGE IVB
  17P GAIN MUTATED           0
  17P GAIN WILD-TYPE        12
D30V39, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  0                 34
  STAGE IB1                 7                 70
  STAGE IB2                 0                 37
  STAGE II                  1                  3
  STAGE IIA                 1                  7
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 5                 39
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                5                 37
  STAGE IVA                 1                  6
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    32   7
  17Q GAIN WILD-TYPE 179  60
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                39                239 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 60 
$`17Q GAIN MUTATED`
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A1MP TCGA-C5-A2LZ 
       23.67        31.40        35.01        35.61         3.58       100.14 
TCGA-C5-A7CH TCGA-C5-A7UE TCGA-DG-A2KH TCGA-DS-A3LQ TCGA-EA-A3HR TCGA-EA-A3QD 
      154.32       155.77         1.12        22.98        30.90        13.05 
TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A3GK 
       31.73        27.22         0.59         0.13        40.96         0.49 
TCGA-EK-A3GM TCGA-EX-A3L1 TCGA-FU-A40J TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-JX-A5QV 
        0.76        15.22        14.01        28.37        44.61        20.91 
TCGA-LP-A4AU TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MY-A913 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       11.28        11.38        28.08        17.23        16.41        15.95 
TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A94X TCGA-VS-A959 TCGA-VS-A9U5 
       93.99        46.52        23.97        16.64        51.32        50.47 
TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UL 
       29.95        24.30        14.53 

$`17Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
        5.46        19.86        67.46        46.32        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       53.16        38.99         0.46         2.43        20.91        40.93 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 
       44.22        73.18        73.45        83.05        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      131.11        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       45.83         8.35       146.86        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.81        20.91        14.73        95.11        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63        69.96 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       95.67        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 
       40.87        37.35        31.53        31.36        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        26.01         0.30        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       14.89        26.79        25.91        27.29        27.25        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.48         0.36        12.59        60.72        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
        1.51        19.27         0.39         0.43         0.36         1.45 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ 
        4.31         0.10         0.43        47.77         0.53         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03        20.35         7.92        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       15.55         1.22        23.84        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26        20.98        26.14         1.48        16.14        28.31 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       35.44        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       129.37        96.95        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AW 
       15.58         8.28        18.15        21.11       209.59         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       12.49         0.30         0.82        13.35        22.52        19.56 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MU-A8JM 
       17.82        19.56         8.35         8.52        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DT 
       54.81        35.05        20.84         2.96        15.58         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PG TCGA-UC-A7PI 
       22.62        19.59        14.60        11.67        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       10.03        45.57        32.42        19.96        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM 
       53.59        36.13        11.51        59.18        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       40.87         4.73        33.37        40.14        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       56.35        55.50        50.14        43.40        48.39        28.50 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO 
       27.12        46.92        45.11         1.71        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
        4.34        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         1.41         0.16         3.91 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.13               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            155.77             210.67 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             23.97              22.52 
[1] "0.1 - 155.8 (24.0)" "0.0 - 210.7 (22.5)"
[1] "hr=" "1.4"
D31V2, continuous
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED    13  12   7   0
  17Q GAIN WILD-TYPE 122  58  14   8
D31V3, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               13                122
  T2               12                 58
  T3                7                 14
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    15   8
  17Q GAIN WILD-TYPE 114  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     15    8
  17Q GAIN WILD-TYPE  114   48
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               15                114
  1                8                 48
[1] 2 2
[1] FALSE
D31V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   16  1
  17Q GAIN WILD-TYPE 92  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     16    1
  17Q GAIN WILD-TYPE   92    9
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               16                 92
  1                1                  9
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     7  18
  17Q GAIN WILD-TYPE  48 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7   18
  17Q GAIN WILD-TYPE   48  105
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 7                 48
  YES               18                105
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED               1                               34
  17Q GAIN WILD-TYPE             5                              208
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17Q GAIN MUTATED                                               1
  17Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17Q GAIN MUTATED                                     6
  17Q GAIN WILD-TYPE                                  15
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17Q GAIN MUTATED                                           0
  17Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17Q GAIN MUTATED                                              0
  17Q GAIN WILD-TYPE                                           17
D31V7, multiclass
                                               clus
vv                                              17Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            34
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              17Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             208
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, continuous
D31V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     4
  17Q GAIN WILD-TYPE                                8    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED                           3
  17Q GAIN WILD-TYPE                        25
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    28
  17Q GAIN WILD-TYPE                                         2   174
D31V10, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                                3                 25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   28                174
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     5  21
  17Q GAIN WILD-TYPE  18 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5   21
  17Q GAIN WILD-TYPE   18  141
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 18
  NOT HISPANIC OR LATINO               21                141
[1] 2 2
[1] FALSE
D31V12, continuous
D31V13, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    25  11
  17Q GAIN WILD-TYPE 158  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     25   11
  17Q GAIN WILD-TYPE  158   63
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  TUMOR FREE               25                158
  WITH TUMOR               11                 63
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  17Q GAIN MUTATED     0  13  25   0   3
  17Q GAIN WILD-TYPE  18 116  90   1  21
D31V14, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  G1                0                 18
  G2               13                116
  G3               25                 90
  G4                0                  1
  GX                3                 21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V15, continuous
D31V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17Q GAIN MUTATED                                             3
  17Q GAIN WILD-TYPE                                          35
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  17Q GAIN MUTATED                                        1
  17Q GAIN WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  17Q GAIN MUTATED                                                 1
  17Q GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17Q GAIN MUTATED                4                  26
  17Q GAIN WILD-TYPE             58                 117
D31V17, multiclass
                                                 clus
vv                                                17Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                           26
                                                 clus
vv                                                17Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     35
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  58
  LIFELONG NON-SMOKER                                            117
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V18, continuous
D31V19, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    4  0
  17Q GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4    0
  17Q GAIN WILD-TYPE   21    3
                         clus
vv                        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D31V20, continuous
D31V21, continuous
D31V22, continuous
D31V23, continuous
D31V24, continuous
D31V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  17Q GAIN MUTATED                                     0
  17Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  17Q GAIN MUTATED                                     1
  17Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  17Q GAIN MUTATED                         4                       0
  17Q GAIN WILD-TYPE                      32                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17Q GAIN MUTATED                         0
  17Q GAIN WILD-TYPE                       8
D31V26, multiclass
                                     clus
vv                                    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                            4                 32
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  17Q GAIN MUTATED                                               0
  17Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  17Q GAIN MUTATED                                                5
  17Q GAIN WILD-TYPE                                             20
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17Q GAIN MUTATED                                                                                  12
  17Q GAIN WILD-TYPE                                                                                70
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17Q GAIN MUTATED                                                                                             15
  17Q GAIN WILD-TYPE                                                                                          106
D31V27, multiclass
                                                                                              clus
vv                                                                                             17Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               15
                                                                                              clus
vv                                                                                             17Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V28, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    8 12
  17Q GAIN WILD-TYPE 63 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      8   12
  17Q GAIN WILD-TYPE   63   62
         clus
vv        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ABSENT                 8                 63
  PRESENT               12                 62
[1] 2 2
[1] FALSE
D31V29, continuous
D31V30, continuous
D31V31, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6  12
  17Q GAIN WILD-TYPE  43 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6   12
  17Q GAIN WILD-TYPE   43  105
                                          clus
vv                                         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               12                105
[1] 2 2
[1] FALSE
D31V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17Q GAIN MUTATED              2           9         10
  17Q GAIN WILD-TYPE           13          45         75
D31V33, multiclass
              clus
vv             17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CURRENT USER                2                 13
  FORMER USER                 9                 45
  NEVER USED                 10                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V34, continuous
D31V35, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   12  4
  17Q GAIN WILD-TYPE 80 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12    4
  17Q GAIN WILD-TYPE   80   14
         clus
vv        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ABSENT                12                 80
  PRESENT                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  17Q GAIN MUTATED             0        15     0
  17Q GAIN WILD-TYPE           5        85     2
D31V36, multiclass
             clus
vv            17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 15                 85
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V37, continuous
D31V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  17Q GAIN MUTATED         0        0         0         0        1        11
  17Q GAIN WILD-TYPE       5        1         1         1       33        66
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  17Q GAIN MUTATED           3        1         2          3          1
  17Q GAIN WILD-TYPE        34        3         6          2          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  17Q GAIN MUTATED           9         0          1          8         0
  17Q GAIN WILD-TYPE        35         1          2         34         7
                    vv
clus                 STAGE IVB
  17Q GAIN MUTATED           0
  17Q GAIN WILD-TYPE        12
D31V39, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  1                 33
  STAGE IB1                11                 66
  STAGE IB2                 3                 34
  STAGE II                  1                  3
  STAGE IIA                 2                  6
  STAGE IIA1                3                  2
  STAGE IIA2                1                  6
  STAGE IIB                 9                 35
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                8                 34
  STAGE IVA                 0                  7
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    37   7
  18P GAIN WILD-TYPE 174  60
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                44                234 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 60 
$`18P GAIN MUTATED`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M7 TCGA-C5-A1MH 
       17.52        17.82        23.67       173.29        46.32        38.99 
TCGA-C5-A2LT TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A8XI 
       73.18       210.67        20.35        17.19       131.11         8.35 
TCGA-DR-A0ZL TCGA-DS-A3LQ TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF 
       87.75        22.98        24.56        31.73        25.91        27.22 
TCGA-EA-A97N TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EX-A8YF TCGA-FU-A3TX TCGA-HM-A3JK 
        0.36         0.59         0.13        15.55         1.48        20.78 
TCGA-JW-A5VK TCGA-JX-A5QV TCGA-MA-AA43 TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R3 
       20.48        20.91        11.38        20.84        17.23        15.95 
TCGA-UC-A7PG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QC TCGA-VS-A953 
       12.16        32.42        23.97        19.96        11.51        15.68 
TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UL TCGA-VS-A9UU TCGA-VS-A9V0 
       50.47        24.30        46.92        14.53        14.53        18.84 
TCGA-XS-A8TJ TCGA-ZJ-AAXU 
       29.26         0.16 

$`18P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       31.40        30.21        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
       52.01        18.02        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
      134.33        15.48       147.35       155.77        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61         2.73        50.99        45.83       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        14.73         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK 
       95.11        82.06        44.94        63.98        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       55.63        69.96        95.67        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B 
       31.36        13.05        25.02        36.89        26.40        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
        0.30        24.82         7.46        14.89        26.79        27.29 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       27.25        24.00        13.48        12.59        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 
        6.64         1.51        19.27         0.39         0.43         0.36 
TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL 
        1.45        40.96         4.31         0.10         0.43        47.77 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
        0.53         0.10         0.49         0.76         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92        15.22        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
       26.14        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 
        1.12        17.75        25.41        16.57        21.67        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        21.44        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        44.61        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        19.56        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         8.35         8.52        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       54.81        35.05         2.96        15.58        16.41         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       22.62        19.59        14.60        11.67        93.99        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       10.03        46.52        45.57        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       36.13        59.18        39.78        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A957 
        4.73        33.37        40.14        58.45        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       50.14        51.32        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       27.12        45.11         1.71        27.25        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.52        26.07        15.85         3.42        18.25        67.20 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 
        5.16        18.25        17.75         4.34        16.24        15.42 
TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       26.01        67.59        19.13         0.69         1.41         3.91 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.13               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            210.67             209.59 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             20.63              24.69 
[1] "0.1 - 210.7 (20.6)" "0.0 - 209.6 (24.7)"
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED    19  10   8   2
  18P GAIN WILD-TYPE 116  60  13   6
D32V3, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               19                116
  T2               10                 60
  T3                8                 13
  T4                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    22   5
  18P GAIN WILD-TYPE 107  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     22    5
  18P GAIN WILD-TYPE  107   51
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               22                107
  1                5                 51
[1] 2 2
[1] FALSE
D32V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   22  2
  18P GAIN WILD-TYPE 86  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     22    2
  18P GAIN WILD-TYPE   86    8
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               22                 86
  1                2                  8
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    8 26
  18P GAIN WILD-TYPE 47 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8   26
  18P GAIN WILD-TYPE   47   97
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 8                 47
  YES               26                 97
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED               1                               45
  18P GAIN WILD-TYPE             5                              197
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18P GAIN MUTATED                                               2
  18P GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18P GAIN MUTATED                                     0
  18P GAIN WILD-TYPE                                  21
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18P GAIN MUTATED                                           0
  18P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18P GAIN MUTATED                                              1
  18P GAIN WILD-TYPE                                           16
D32V7, multiclass
                                               clus
vv                                              18P GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            45
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              18P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             197
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, continuous
D32V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  1     3
  18P GAIN WILD-TYPE                                7    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED                           5
  18P GAIN WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           0    31
  18P GAIN WILD-TYPE                                         2   171
D32V10, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                5                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   31                171
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     5  23
  18P GAIN WILD-TYPE  18 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5   23
  18P GAIN WILD-TYPE   18  139
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 18
  NOT HISPANIC OR LATINO               23                139
[1] 2 2
[1] FALSE
D32V12, continuous
D32V13, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    31  11
  18P GAIN WILD-TYPE 152  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     31   11
  18P GAIN WILD-TYPE  152   63
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  TUMOR FREE               31                152
  WITH TUMOR               11                 63
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  18P GAIN MUTATED     4  14  26   0   3
  18P GAIN WILD-TYPE  14 115  89   1  21
D32V14, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  G1                4                 14
  G2               14                115
  G3               26                 89
  G4                0                  1
  GX                3                 21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V15, continuous
D32V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18P GAIN MUTATED                                             7
  18P GAIN WILD-TYPE                                          31
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  18P GAIN MUTATED                                        3
  18P GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  18P GAIN MUTATED                                                 2
  18P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18P GAIN MUTATED                8                  21
  18P GAIN WILD-TYPE             54                 122
D32V17, multiclass
                                                 clus
vv                                                18P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                2
  CURRENT SMOKER                                                 8
  LIFELONG NON-SMOKER                                           21
                                                 clus
vv                                                18P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  54
  LIFELONG NON-SMOKER                                            122
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V18, continuous
D32V19, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4  0
  18P GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    0
  18P GAIN WILD-TYPE   21    3
                         clus
vv                        18P GAIN MUTATED 18P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D32V20, continuous
D32V21, continuous
D32V22, continuous
D32V23, continuous
D32V24, continuous
D32V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  18P GAIN MUTATED                                     2
  18P GAIN WILD-TYPE                                   1
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  18P GAIN MUTATED                                     1
  18P GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  18P GAIN MUTATED                         7                       0
  18P GAIN WILD-TYPE                      29                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18P GAIN MUTATED                         0
  18P GAIN WILD-TYPE                       8
D32V26, multiclass
                                     clus
vv                                    18P GAIN MUTATED 18P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                2                  1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                            7                 29
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  18P GAIN MUTATED                                               0
  18P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18P GAIN MUTATED                                                5
  18P GAIN WILD-TYPE                                             20
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18P GAIN MUTATED                                                                                  14
  18P GAIN WILD-TYPE                                                                                68
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18P GAIN MUTATED                                                                                             18
  18P GAIN WILD-TYPE                                                                                          103
D32V27, multiclass
                                                                                              clus
vv                                                                                             18P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               18
                                                                                              clus
vv                                                                                             18P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V28, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   10 11
  18P GAIN WILD-TYPE 61 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     10   11
  18P GAIN WILD-TYPE   61   63
         clus
vv        18P GAIN MUTATED 18P GAIN WILD-TYPE
  ABSENT                10                 61
  PRESENT               11                 63
[1] 2 2
[1] FALSE
D32V29, continuous
D32V30, continuous
D32V31, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    9 23
  18P GAIN WILD-TYPE 40 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      9   23
  18P GAIN WILD-TYPE   40   94
                                          clus
vv                                         18P GAIN MUTATED 18P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               23                 94
[1] 2 2
[1] FALSE
D32V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18P GAIN MUTATED              2           7         19
  18P GAIN WILD-TYPE           13          47         66
D32V33, multiclass
              clus
vv             18P GAIN MUTATED 18P GAIN WILD-TYPE
  CURRENT USER                2                 13
  FORMER USER                 7                 47
  NEVER USED                 19                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V34, continuous
D32V35, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   12  3
  18P GAIN WILD-TYPE 80 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     12    3
  18P GAIN WILD-TYPE   80   15
         clus
vv        18P GAIN MUTATED 18P GAIN WILD-TYPE
  ABSENT                12                 80
  PRESENT                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  18P GAIN MUTATED             0        21     0
  18P GAIN WILD-TYPE           5        79     2
D32V36, multiclass
             clus
vv            18P GAIN MUTATED 18P GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 21                 79
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V37, continuous
D32V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  18P GAIN MUTATED         0        0         0         0        7         7
  18P GAIN WILD-TYPE       5        1         1         1       27        70
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  18P GAIN MUTATED           9        0         1          1          2
  18P GAIN WILD-TYPE        28        4         7          4          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  18P GAIN MUTATED           8         0          1          8         3
  18P GAIN WILD-TYPE        36         1          2         34         4
                    vv
clus                 STAGE IVB
  18P GAIN MUTATED           0
  18P GAIN WILD-TYPE        12
D32V39, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  7                 27
  STAGE IB1                 7                 70
  STAGE IB2                 9                 28
  STAGE II                  0                  4
  STAGE IIA                 1                  7
  STAGE IIA1                1                  4
  STAGE IIA2                2                  5
  STAGE IIB                 8                 36
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                8                 34
  STAGE IVA                 3                  4
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    22   5
  18Q GAIN WILD-TYPE 189  62
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                27                251 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 62 
$`18Q GAIN MUTATED`
TCGA-2W-A8YY TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A7CG TCGA-C5-A7UH TCGA-C5-A8XI 
       17.52        38.99        73.18       210.67       131.11         8.35 
TCGA-DS-A3LQ TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2R9 
       22.98        24.56        31.73        27.22         0.36         0.13 
TCGA-FU-A3TX TCGA-HM-A3JK TCGA-JW-A5VK TCGA-JX-A5QV TCGA-MA-AA43 TCGA-MY-A913 
        1.48        20.78        20.48        20.91        11.38        17.23 
TCGA-UC-A7PG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8QC TCGA-VS-A953 TCGA-VS-A9UL 
       12.16        32.42        23.97        11.51        15.68        14.53 
TCGA-VS-A9UU TCGA-XS-A8TJ TCGA-ZJ-AAXU 
       14.53        29.26         0.16 

$`18Q GAIN WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.82        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       35.01        57.73        53.16        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93         3.58        44.22        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35       147.35        17.19       155.77        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK 
       13.61         2.73        50.99        45.83       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        14.73         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       95.11        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76        55.63        69.96        95.67        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       17.52         8.28        39.55        40.87        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       25.91        27.29        27.25        24.00        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
       60.72        26.27         6.64         1.51        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RC 
        0.43         0.59         0.36         1.45        40.96         4.31 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.10         0.43        47.77         0.53         0.10         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.76         0.03        20.35         7.92        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         8.32        15.55         1.22        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
       16.11        31.36        36.26        20.98        26.14        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       28.31        14.01        35.44        10.55         1.12        17.75 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        16.57        21.67        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       129.37        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        28.37         8.28        18.15        21.11       209.59 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       44.61        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
       13.35        22.52        19.56        17.82        19.56         8.35 
TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        8.52        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       22.62        19.59        14.60        11.67        93.99        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       10.03        46.52        45.57        19.96        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       53.59        36.13        59.18        39.78        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 
       16.64         4.73        33.37        40.14        58.45        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       55.50        50.14        51.32        50.47        43.40        48.39 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       28.50        29.95        27.12        24.30        46.92        45.11 
TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
        1.71        27.25        47.87        47.47        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 
       15.85         3.42        18.25        67.20        18.84         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
       18.25        17.75         4.34        16.24        15.42        26.01 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       67.59        19.13         0.69         1.41         3.91 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.13               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            210.67             209.59 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             20.48              24.00 
[1] "0.1 - 210.7 (20.5)" "0.0 - 209.6 (24.0)"
[1] "hr=" "1.1"
D33V2, continuous
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED    12   6   7   1
  18Q GAIN WILD-TYPE 123  64  14   7
D33V3, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               12                123
  T2                6                 64
  T3                7                 14
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    14   5
  18Q GAIN WILD-TYPE 115  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     14    5
  18Q GAIN WILD-TYPE  115   51
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               14                115
  1                5                 51
[1] 2 2
[1] FALSE
D33V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED   16  1
  18Q GAIN WILD-TYPE 92  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     16    1
  18Q GAIN WILD-TYPE   92    9
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               16                 92
  1                1                  9
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5  16
  18Q GAIN WILD-TYPE  50 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5   16
  18Q GAIN WILD-TYPE   50  107
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 5                 50
  YES               16                107
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED               1                               30
  18Q GAIN WILD-TYPE             5                              212
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18Q GAIN MUTATED                                               1
  18Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18Q GAIN MUTATED                                     0
  18Q GAIN WILD-TYPE                                  21
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18Q GAIN MUTATED                                           0
  18Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18Q GAIN MUTATED                                              0
  18Q GAIN WILD-TYPE                                           17
D33V7, multiclass
                                               clus
vv                                              18Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              18Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             212
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, continuous
D33V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  1     2
  18Q GAIN WILD-TYPE                                7    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED                           4
  18Q GAIN WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           0    17
  18Q GAIN WILD-TYPE                                         2   185
D33V10, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                4                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   17                185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4  15
  18Q GAIN WILD-TYPE  19 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4   15
  18Q GAIN WILD-TYPE   19  147
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 19
  NOT HISPANIC OR LATINO               15                147
[1] 2 2
[1] FALSE
D33V12, continuous
D33V13, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    18   7
  18Q GAIN WILD-TYPE 165  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     18    7
  18Q GAIN WILD-TYPE  165   67
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  TUMOR FREE               18                165
  WITH TUMOR                7                 67
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  18Q GAIN MUTATED     3   8  17   0   2
  18Q GAIN WILD-TYPE  15 121  98   1  22
D33V14, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  G1                3                 15
  G2                8                121
  G3               17                 98
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, continuous
D33V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18Q GAIN MUTATED                                             4
  18Q GAIN WILD-TYPE                                          34
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  18Q GAIN MUTATED                                        3
  18Q GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  18Q GAIN MUTATED                                                 2
  18Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18Q GAIN MUTATED                7                  11
  18Q GAIN WILD-TYPE             55                 132
D33V17, multiclass
                                                 clus
vv                                                18Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                2
  CURRENT SMOKER                                                 7
  LIFELONG NON-SMOKER                                           11
                                                 clus
vv                                                18Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     34
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  55
  LIFELONG NON-SMOKER                                            132
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V18, continuous
D33V19, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  0
  18Q GAIN WILD-TYPE 22  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    0
  18Q GAIN WILD-TYPE   22    3
                         clus
vv                        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   3                 22
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D33V20, continuous
D33V21, continuous
D33V22, continuous
D33V23, continuous
D33V24, continuous
D33V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  18Q GAIN MUTATED                                     2
  18Q GAIN WILD-TYPE                                   1
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  18Q GAIN MUTATED                                     0
  18Q GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  18Q GAIN MUTATED                         5                       0
  18Q GAIN WILD-TYPE                      31                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18Q GAIN MUTATED                         0
  18Q GAIN WILD-TYPE                       8
D33V26, multiclass
                                     clus
vv                                    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                2                  1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            5                 31
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  18Q GAIN MUTATED                                               0
  18Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18Q GAIN MUTATED                                                4
  18Q GAIN WILD-TYPE                                             21
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18Q GAIN MUTATED                                                                                   8
  18Q GAIN WILD-TYPE                                                                                74
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18Q GAIN MUTATED                                                                                             12
  18Q GAIN WILD-TYPE                                                                                          109
D33V27, multiclass
                                                                                              clus
vv                                                                                             18Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               12
                                                                                              clus
vv                                                                                             18Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            74
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V28, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    7  6
  18Q GAIN WILD-TYPE 64 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    6
  18Q GAIN WILD-TYPE   64   68
         clus
vv        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ABSENT                 7                 64
  PRESENT                6                 68
[1] 2 2
[1] FALSE
D33V29, continuous
D33V30, continuous
D33V31, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     7  14
  18Q GAIN WILD-TYPE  42 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7   14
  18Q GAIN WILD-TYPE   42  103
                                          clus
vv                                         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    7                 42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               14                103
[1] 2 2
[1] FALSE
D33V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18Q GAIN MUTATED              2           6         10
  18Q GAIN WILD-TYPE           13          48         75
D33V33, multiclass
              clus
vv             18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CURRENT USER                2                 13
  FORMER USER                 6                 48
  NEVER USED                 10                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V34, continuous
D33V35, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    7  2
  18Q GAIN WILD-TYPE 85 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7    2
  18Q GAIN WILD-TYPE   85   16
         clus
vv        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ABSENT                 7                 85
  PRESENT                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  18Q GAIN MUTATED             0        14     0
  18Q GAIN WILD-TYPE           5        86     2
D33V36, multiclass
             clus
vv            18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 14                 86
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V37, continuous
D33V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  18Q GAIN MUTATED         0        0         0         0        2         5
  18Q GAIN WILD-TYPE       5        1         1         1       32        72
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  18Q GAIN MUTATED           6        0         1          1          1
  18Q GAIN WILD-TYPE        31        4         7          4          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  18Q GAIN MUTATED           5         0          0          8         2
  18Q GAIN WILD-TYPE        39         1          3         34         5
                    vv
clus                 STAGE IVB
  18Q GAIN MUTATED           0
  18Q GAIN WILD-TYPE        12
D33V39, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  2                 32
  STAGE IB1                 5                 72
  STAGE IB2                 6                 31
  STAGE II                  0                  4
  STAGE IIA                 1                  7
  STAGE IIA1                1                  4
  STAGE IIA2                1                  6
  STAGE IIB                 5                 39
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB                8                 34
  STAGE IVA                 2                  5
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    34   7
  19P GAIN WILD-TYPE 177  60
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                41                237 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                 60 
$`19P GAIN MUTATED`
TCGA-C5-A0TN TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A7CG 
       11.44        53.16        38.99        78.35        52.01       210.67 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7X5 TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KL 
      154.32       134.33        13.61        14.73        95.11        44.94 
TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EA-A97N 
       55.63        22.98         8.28        25.91        27.22         0.36 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RN TCGA-FU-A40J TCGA-HG-A9SC TCGA-HM-A3JK 
        0.59         0.36         0.53        14.01        16.57        20.78 
TCGA-IR-A3LL TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BE 
       36.36       209.59        11.28         0.30        13.35        35.05 
TCGA-MY-A913 TCGA-Q1-A5R3 TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A953 
       17.23        15.95        12.16        23.97        59.18        15.68 
TCGA-VS-A954 TCGA-VS-A9U5 TCGA-VS-A9UU TCGA-WL-A834 TCGA-ZJ-AAXA 
       56.35        50.47        14.53        26.01         1.41 

$`19P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        23.67        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       35.01        57.73        35.61         0.46         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       40.93         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43        33.24        18.02        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82        15.48        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
      131.11        94.95         9.34         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35       146.86        99.91        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       20.91         1.12        82.06        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       36.76        69.96        95.67        16.83        16.18        17.52 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       27.29        27.25        24.00        13.48        12.59        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL 
       26.27         6.64         1.51        19.27         0.39         0.43 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK 
        1.45         0.13        40.96         4.31         0.10         0.43 
TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
       47.77         0.10         0.49         0.76         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        7.92        15.22        14.70        19.79         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
       20.98        26.14         1.48        16.14        28.31        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 
       10.55         1.12        17.75        25.41        21.67        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        29.85        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       21.11        44.61        20.91         0.89        12.49         0.82 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        19.56        17.82        19.56         8.35         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF 
       11.38        28.08        34.62        19.96        54.81        20.84 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96        15.58        16.41         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       14.60        11.67        93.99        69.50        10.03        46.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       45.57        32.42        19.96        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       36.13        11.51        39.78        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 
        4.73        33.37        40.14        58.45        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       51.32        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       24.30        46.92        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV 
       47.87        47.47        41.52        26.07        15.85         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
        4.34        16.24        15.42        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         0.16         3.91 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.30               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            210.67             177.04 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             22.98              23.51 
[1] "0.3 - 210.7 (23.0)" "0.0 - 177.0 (23.5)"
[1] "hr=" "1.6"
D34V2, continuous
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED    14  12   6   1
  19P GAIN WILD-TYPE 121  58  15   7
D34V3, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               14                121
  T2               12                 58
  T3                6                 15
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    16  12
  19P GAIN WILD-TYPE 113  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16   12
  19P GAIN WILD-TYPE  113   44
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               16                113
  1               12                 44
[1] 2 2
[1] FALSE
D34V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   16  1
  19P GAIN WILD-TYPE 92  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16    1
  19P GAIN WILD-TYPE   92    9
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               16                 92
  1                1                  9
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     7  22
  19P GAIN WILD-TYPE  48 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7   22
  19P GAIN WILD-TYPE   48  101
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 7                 48
  YES               22                101
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED               1                               40
  19P GAIN WILD-TYPE             5                              202
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19P GAIN MUTATED                                               1
  19P GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19P GAIN MUTATED                                     2
  19P GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19P GAIN MUTATED                                           0
  19P GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19P GAIN MUTATED                                              0
  19P GAIN WILD-TYPE                                           17
D34V7, multiclass
                                               clus
vv                                              19P GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            40
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              19P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             202
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, continuous
D34V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     4
  19P GAIN WILD-TYPE                                8    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED                           5
  19P GAIN WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           0    27
  19P GAIN WILD-TYPE                                         2   175
D34V10, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                                5                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   27                175
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  26
  19P GAIN WILD-TYPE  22 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   26
  19P GAIN WILD-TYPE   22  136
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 22
  NOT HISPANIC OR LATINO               26                136
[1] 2 2
[1] FALSE
D34V12, continuous
D34V13, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    30   9
  19P GAIN WILD-TYPE 153  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     30    9
  19P GAIN WILD-TYPE  153   65
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  TUMOR FREE               30                153
  WITH TUMOR                9                 65
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  19P GAIN MUTATED     3  20  19   0   2
  19P GAIN WILD-TYPE  15 109  96   1  22
D34V14, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  G1                3                 15
  G2               20                109
  G3               19                 96
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, continuous
D34V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19P GAIN MUTATED                                             7
  19P GAIN WILD-TYPE                                          31
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  19P GAIN MUTATED                                        3
  19P GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  19P GAIN MUTATED                                                 2
  19P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19P GAIN MUTATED                3                  21
  19P GAIN WILD-TYPE             59                 122
D34V17, multiclass
                                                 clus
vv                                                19P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                2
  CURRENT SMOKER                                                 3
  LIFELONG NON-SMOKER                                           21
                                                 clus
vv                                                19P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  59
  LIFELONG NON-SMOKER                                            122
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V18, continuous
D34V19, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    5  1
  19P GAIN WILD-TYPE 20  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      5    1
  19P GAIN WILD-TYPE   20    2
                         clus
vv                        19P GAIN MUTATED 19P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   5                 20
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D34V20, continuous
D34V21, continuous
D34V22, continuous
D34V23, continuous
D34V24, continuous
D34V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  19P GAIN MUTATED                                     0
  19P GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  19P GAIN MUTATED                                     2
  19P GAIN WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  19P GAIN MUTATED                         5                       0
  19P GAIN WILD-TYPE                      31                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19P GAIN MUTATED                         1
  19P GAIN WILD-TYPE                       7
D34V26, multiclass
                                     clus
vv                                    19P GAIN MUTATED 19P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  5
  OTHER LOCATION, SPECIFY                            5                 31
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  19P GAIN MUTATED                                               0
  19P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  19P GAIN MUTATED                                                2
  19P GAIN WILD-TYPE                                             23
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19P GAIN MUTATED                                                                                  12
  19P GAIN WILD-TYPE                                                                                70
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19P GAIN MUTATED                                                                                             19
  19P GAIN WILD-TYPE                                                                                          102
D34V27, multiclass
                                                                                              clus
vv                                                                                             19P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               19
                                                                                              clus
vv                                                                                             19P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V28, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    7 15
  19P GAIN WILD-TYPE 64 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7   15
  19P GAIN WILD-TYPE   64   59
         clus
vv        19P GAIN MUTATED 19P GAIN WILD-TYPE
  ABSENT                 7                 64
  PRESENT               15                 59
[1] 2 2
[1] FALSE
D34V29, continuous
D34V30, continuous
D34V31, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    12  13
  19P GAIN WILD-TYPE  37 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     12   13
  19P GAIN WILD-TYPE   37  104
                                          clus
vv                                         19P GAIN MUTATED 19P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   12                 37
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               13                104
[1] 2 2
[1] FALSE
D34V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19P GAIN MUTATED              2           8         13
  19P GAIN WILD-TYPE           13          46         72
D34V33, multiclass
              clus
vv             19P GAIN MUTATED 19P GAIN WILD-TYPE
  CURRENT USER                2                 13
  FORMER USER                 8                 46
  NEVER USED                 13                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V34, continuous
D34V35, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   13  0
  19P GAIN WILD-TYPE 79 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     13    0
  19P GAIN WILD-TYPE   79   18
         clus
vv        19P GAIN MUTATED 19P GAIN WILD-TYPE
  ABSENT                13                 79
  PRESENT                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  19P GAIN MUTATED             1        18     0
  19P GAIN WILD-TYPE           4        82     2
D34V36, multiclass
             clus
vv            19P GAIN MUTATED 19P GAIN WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 18                 82
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V37, continuous
D34V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  19P GAIN MUTATED         0        0         0         0        4         6
  19P GAIN WILD-TYPE       5        1         1         1       30        71
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  19P GAIN MUTATED           5        1         2          0          2
  19P GAIN WILD-TYPE        32        3         6          5          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  19P GAIN MUTATED           9         1          0          9         2
  19P GAIN WILD-TYPE        35         0          3         33         5
                    vv
clus                 STAGE IVB
  19P GAIN MUTATED           1
  19P GAIN WILD-TYPE        11
D34V39, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  4                 30
  STAGE IB1                 6                 71
  STAGE IB2                 5                 32
  STAGE II                  1                  3
  STAGE IIA                 2                  6
  STAGE IIA1                0                  5
  STAGE IIA2                2                  5
  STAGE IIB                 9                 35
  STAGE III                 1                  0
  STAGE IIIA                0                  3
  STAGE IIIB                9                 33
  STAGE IVA                 2                  5
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    50  15
  19Q GAIN WILD-TYPE 161  52
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                65                213 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                15                 52 
$`19Q GAIN MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       23.67        11.44         5.46        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A7CG 
       35.61         2.43        73.18        78.35        52.01       210.67 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7X3 TCGA-C5-A8XH TCGA-C5-A8YR 
      154.32       134.33       147.35         9.34        45.83        27.52 
TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WI 
       14.73        95.11        44.94        55.63        22.98         8.28 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZF 
       36.89        24.56        31.73        26.01        25.91        27.22 
TCGA-EA-A97N TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RA 
        0.36         0.39         0.43         0.59         0.36        40.96 
TCGA-EK-A2RN TCGA-FU-A40J TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LL 
        0.53        14.01        16.57        21.67        20.78        36.36 
TCGA-JX-A3Q0 TCGA-LP-A5U2 TCGA-LP-A7HU TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R3 
      209.59         0.30        13.35        35.05         2.96        15.95 
TCGA-UC-A7PG TCGA-VS-A8EI TCGA-VS-A8QF TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A953 
       12.16        23.97        59.18        40.87        16.64        15.68 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UD 
       56.35        50.14        51.32        50.47        28.50        24.30 
TCGA-VS-A9UI TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9UU TCGA-ZJ-AAXA 
       45.11        47.47        15.85        14.53         1.41 

$`19Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF 
       17.52        17.82        49.48        57.04        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ 
       36.56       144.16       177.04       173.29        82.85        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MJ 
       67.46        31.40        46.32        30.21        35.01         0.46 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91        40.93         3.58        44.22        73.45        83.05 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43        33.24        18.02        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
      101.82        15.48        20.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
       94.95        13.61         2.73        50.99         8.35       146.86 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KH TCGA-DG-A2KK 
       99.91        23.51        20.81        20.91         1.12        82.06 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       63.98        87.75        58.88        36.76        69.96        95.67 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18        17.52        39.55        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 
       30.90        31.53        31.36        13.05        25.02        26.40 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
        0.30        24.82         7.46        14.89        26.79        27.29 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       27.25        24.00        13.48        12.59        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC 
        6.64         1.51        19.27         1.45         0.13         4.31 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM 
        0.10         0.43        47.77         0.10         0.49         0.76 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92        15.22        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        8.32        15.55         1.22        23.84        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       31.36        36.26        20.98        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       28.31        35.44        10.55         1.12        17.75        25.41 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        78.71        81.96        29.85        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       18.15        21.11        44.61        20.91        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
       12.49         0.82        22.52        19.56        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        8.35         8.52        11.38        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       54.81        20.84        17.23        15.58        16.41         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       22.62        19.59        14.60        11.67        93.99        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        46.52        45.57        32.42        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM 
       32.15        53.59        36.13        11.51        39.78        31.27 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A9U6 
        4.73        33.37        40.14        58.45        55.50        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL 
       48.39        29.95        27.12        46.92         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY 
       27.25        47.87        41.52        26.07         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       67.20        18.84         5.16        18.25        17.75         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         0.16         3.91 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.30               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            210.67             177.04 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             26.01              20.91 
[1] "0.3 - 210.7 (26.0)" "0.0 - 177.0 (20.9)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED    26  21   9   1
  19Q GAIN WILD-TYPE 109  49  12   7
D35V3, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               26                109
  T2               21                 49
  T3                9                 12
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    28  16
  19Q GAIN WILD-TYPE 101  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     28   16
  19Q GAIN WILD-TYPE  101   40
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               28                101
  1               16                 40
[1] 2 2
[1] FALSE
D35V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   27  0
  19Q GAIN WILD-TYPE 81 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     27    0
  19Q GAIN WILD-TYPE   81   10
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               27                 81
  1                0                 10
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   11 31
  19Q GAIN WILD-TYPE 44 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     11   31
  19Q GAIN WILD-TYPE   44   92
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                11                 44
  YES               31                 92
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED               1                               64
  19Q GAIN WILD-TYPE             5                              178
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19Q GAIN MUTATED                                               2
  19Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19Q GAIN MUTATED                                     3
  19Q GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19Q GAIN MUTATED                                           0
  19Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19Q GAIN MUTATED                                              2
  19Q GAIN WILD-TYPE                                           15
D35V7, multiclass
                                               clus
vv                                              19Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            64
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              19Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             178
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, continuous
D35V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     5
  19Q GAIN WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED                           6
  19Q GAIN WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           0    50
  19Q GAIN WILD-TYPE                                         2   152
D35V10, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                                6                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   50                152
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  44
  19Q GAIN WILD-TYPE  22 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   44
  19Q GAIN WILD-TYPE   22  118
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 22
  NOT HISPANIC OR LATINO               44                118
[1] 2 2
[1] FALSE
D35V12, continuous
D35V13, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    44  17
  19Q GAIN WILD-TYPE 139  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     44   17
  19Q GAIN WILD-TYPE  139   57
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  TUMOR FREE               44                139
  WITH TUMOR               17                 57
[1] 2 2
[1] FALSE
                    vv
clus                 G1 G2 G3 G4 GX
  19Q GAIN MUTATED    4 30 32  0  3
  19Q GAIN WILD-TYPE 14 99 83  1 21
D35V14, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  G1                4                 14
  G2               30                 99
  G3               32                 83
  G4                0                  1
  GX                3                 21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, continuous
D35V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19Q GAIN MUTATED                                            11
  19Q GAIN WILD-TYPE                                          27
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  19Q GAIN MUTATED                                        4
  19Q GAIN WILD-TYPE                                      5
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  19Q GAIN MUTATED                                                 1
  19Q GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19Q GAIN MUTATED                7                  36
  19Q GAIN WILD-TYPE             55                 107
D35V17, multiclass
                                                 clus
vv                                                19Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 7
  LIFELONG NON-SMOKER                                           36
                                                 clus
vv                                                19Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  55
  LIFELONG NON-SMOKER                                            107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V18, continuous
D35V19, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    9  2
  19Q GAIN WILD-TYPE 16  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9    2
  19Q GAIN WILD-TYPE   16    1
                         clus
vv                        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                2                  1
[1] 2 2
[1] FALSE
D35V20, continuous
D35V21, continuous
D35V22, continuous
D35V23, continuous
D35V24, continuous
D35V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  19Q GAIN MUTATED                                     0
  19Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  19Q GAIN MUTATED                                     2
  19Q GAIN WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  19Q GAIN MUTATED                         9                       0
  19Q GAIN WILD-TYPE                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19Q GAIN MUTATED                         1
  19Q GAIN WILD-TYPE                       7
D35V26, multiclass
                                     clus
vv                                    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  5
  OTHER LOCATION, SPECIFY                            9                 27
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  19Q GAIN MUTATED                                               0
  19Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  19Q GAIN MUTATED                                                4
  19Q GAIN WILD-TYPE                                             21
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19Q GAIN MUTATED                                                                                  20
  19Q GAIN WILD-TYPE                                                                                62
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19Q GAIN MUTATED                                                                                             26
  19Q GAIN WILD-TYPE                                                                                           95
D35V27, multiclass
                                                                                              clus
vv                                                                                             19Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               26
                                                                                              clus
vv                                                                                             19Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            62
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V28, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   13 20
  19Q GAIN WILD-TYPE 58 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13   20
  19Q GAIN WILD-TYPE   58   54
         clus
vv        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ABSENT                13                 58
  PRESENT               20                 54
[1] 2 2
[1] FALSE
D35V29, continuous
D35V30, continuous
D35V31, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   17 25
  19Q GAIN WILD-TYPE 32 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     17   25
  19Q GAIN WILD-TYPE   32   92
                                          clus
vv                                         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   17                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               25                 92
[1] 2 2
[1] FALSE
D35V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19Q GAIN MUTATED              3          11         25
  19Q GAIN WILD-TYPE           12          43         60
D35V33, multiclass
              clus
vv             19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CURRENT USER                3                 12
  FORMER USER                11                 43
  NEVER USED                 25                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V34, continuous
D35V35, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   18  3
  19Q GAIN WILD-TYPE 74 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     18    3
  19Q GAIN WILD-TYPE   74   15
         clus
vv        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ABSENT                18                 74
  PRESENT                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  19Q GAIN MUTATED             1        29     0
  19Q GAIN WILD-TYPE           4        71     2
D35V36, multiclass
             clus
vv            19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 29                 71
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V37, continuous
D35V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  19Q GAIN MUTATED         0        0         0         0        8        14
  19Q GAIN WILD-TYPE       5        1         1         1       26        63
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  19Q GAIN MUTATED           9        1         2          1          3
  19Q GAIN WILD-TYPE        28        3         6          4          4
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  19Q GAIN MUTATED          16         1          2         12         2
  19Q GAIN WILD-TYPE        28         0          1         30         5
                    vv
clus                 STAGE IVB
  19Q GAIN MUTATED           0
  19Q GAIN WILD-TYPE        12
D35V39, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  8                 26
  STAGE IB1                14                 63
  STAGE IB2                 9                 28
  STAGE II                  1                  3
  STAGE IIA                 2                  6
  STAGE IIA1                1                  4
  STAGE IIA2                3                  4
  STAGE IIB                16                 28
  STAGE III                 1                  0
  STAGE IIIA                2                  1
  STAGE IIIB               12                 30
  STAGE IVA                 2                  5
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    71  24
  20P GAIN WILD-TYPE 140  43
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                95                183 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                24                 43 
$`20P GAIN MUTATED`
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MI 
      144.16       173.29        67.46        31.40        35.01        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LZ 
        0.46        40.93         3.58        73.18        73.45       100.14 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
      210.67       154.32        20.35       147.35        17.19       131.11 
TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DS-A0VK 
        2.73        27.52         1.12        95.11        63.98        36.76 
TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3QD 
       22.98        17.52        39.55        37.35        31.53        13.05 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N 
       31.73        14.89        26.79        27.22        24.00         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 
       12.59        26.27         1.51         0.59         0.36         0.13 
TCGA-EK-A2RA TCGA-EK-A3GM TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI 
       40.96         0.76         1.22        23.84        16.11        20.98 
TCGA-FU-A40J TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-JW-A5VK 
       14.01        21.67        20.78       147.39        96.95        20.48 
TCGA-JW-A69B TCGA-JX-A3Q0 TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA43 
       28.37       209.59        12.49        13.35        19.56        11.38 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW 
        2.96        15.58        16.41        15.95         9.04        17.56 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC 
       22.62        14.60        93.99        12.16        69.50        46.52 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W 
       23.97        19.96        36.13        11.51        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A959 TCGA-VS-A9UD 
       16.64        40.14        15.68        56.35        51.32        24.30 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UU 
       46.92        45.11        14.53        27.25        47.47        14.53 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-WL-A834 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       17.75         4.34        26.01         1.41         0.16 

$`20P GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN 
       68.84        18.74        36.56       177.04        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       19.86        46.32        30.21        57.73        53.16        38.99 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 
        2.43        20.91        44.22        83.05        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ 
       33.24        52.01        18.02        17.85        20.42       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
      134.33        15.48       155.77        94.95         9.34        13.61 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
       50.99        45.83         8.35       146.86        99.91        23.51 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZL 
       20.81        20.91        14.73        82.06        44.94        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88        55.63        69.96        95.67        16.83        16.18 
TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 
        8.28        40.87        30.90        31.36        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        26.01         0.30        24.82         7.46 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP 
       25.91        27.29        27.25        13.48        60.72         6.64 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2RC TCGA-EK-A2RD 
       19.27         0.39         0.43         1.45         4.31         0.10 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        0.43        47.77         0.53         0.10         0.49         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92        15.22        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
       15.55        19.04        31.36        36.26        26.14         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       16.14        28.31        35.44        10.55         1.12        17.75 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
       25.41        16.57        14.93         9.44       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      129.37        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH 
        3.29        24.56        21.44        15.58         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 
       21.11        44.61        20.91        11.28         0.89         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
        0.82        22.52        17.82        19.56         8.35         8.52 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       28.08        34.62        19.96        54.81        35.05        20.84 
TCGA-MY-A913 TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       17.23        16.14        14.07        15.88         9.34        18.64 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL 
       19.59        11.67        10.03        45.57        32.42        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z 
       32.15        53.59        59.18        39.78         4.73        33.37 
TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       58.45        55.50        50.14        50.47        43.40        48.39 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ 
       28.50        29.95        27.12         1.71        47.87        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       26.07        15.85         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
        5.16        18.25        16.24        15.42        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZX-AA5X 
       19.13         0.69         3.91 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.13               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            210.67             177.04 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             23.84              22.52 
[1] "0.1 - 210.7 (23.8)" "0.0 - 177.0 (22.5)"
[1] "hr=" "1"  
D36V2, continuous
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED   41 19 14  4
  20P GAIN WILD-TYPE 94 51  7  4
D36V3, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               41                 94
  T2               19                 51
  T3               14                  7
  T4                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   34 22
  20P GAIN WILD-TYPE 95 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     34   22
  20P GAIN WILD-TYPE   95   34
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               34                 95
  1               22                 34
[1] 2 2
[1] FALSE
D36V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   36  2
  20P GAIN WILD-TYPE 72  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     36    2
  20P GAIN WILD-TYPE   72    8
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               36                 72
  1                2                  8
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   14 45
  20P GAIN WILD-TYPE 41 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     14   45
  20P GAIN WILD-TYPE   41   78
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                14                 41
  YES               45                 78
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED               2                               81
  20P GAIN WILD-TYPE             4                              161
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20P GAIN MUTATED                                               3
  20P GAIN WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20P GAIN MUTATED                                     7
  20P GAIN WILD-TYPE                                  14
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20P GAIN MUTATED                                           2
  20P GAIN WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20P GAIN MUTATED                                              5
  20P GAIN WILD-TYPE                                           12
D36V7, multiclass
                                               clus
vv                                              20P GAIN MUTATED
  ADENOSQUAMOUS                                                2
  CERVICAL SQUAMOUS CELL CARCINOMA                            81
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 5
                                               clus
vv                                              20P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             161
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, continuous
D36V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     5
  20P GAIN WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED                          12
  20P GAIN WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           0    67
  20P GAIN WILD-TYPE                                         2   135
D36V10, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                               12                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   67                135
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     5  55
  20P GAIN WILD-TYPE  18 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5   55
  20P GAIN WILD-TYPE   18  107
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 18
  NOT HISPANIC OR LATINO               55                107
[1] 2 2
[1] FALSE
D36V12, continuous
D36V13, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    60  26
  20P GAIN WILD-TYPE 123  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     60   26
  20P GAIN WILD-TYPE  123   48
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  TUMOR FREE               60                123
  WITH TUMOR               26                 48
[1] 2 2
[1] FALSE
                    vv
clus                 G1 G2 G3 G4 GX
  20P GAIN MUTATED    4 41 44  0 11
  20P GAIN WILD-TYPE 14 88 71  1 13
D36V14, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  G1                4                 14
  G2               41                 88
  G3               44                 71
  G4                0                  1
  GX               11                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, continuous
D36V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20P GAIN MUTATED                                            15
  20P GAIN WILD-TYPE                                          23
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  20P GAIN MUTATED                                        4
  20P GAIN WILD-TYPE                                      5
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  20P GAIN MUTATED                                                 0
  20P GAIN WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20P GAIN MUTATED               17                  49
  20P GAIN WILD-TYPE             45                  94
D36V17, multiclass
                                                 clus
vv                                                20P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                17
  LIFELONG NON-SMOKER                                           49
                                                 clus
vv                                                20P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     23
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  45
  LIFELONG NON-SMOKER                                             94
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V18, continuous
D36V19, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    9  0
  20P GAIN WILD-TYPE 16  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      9    0
  20P GAIN WILD-TYPE   16    3
                         clus
vv                        20P GAIN MUTATED 20P GAIN WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D36V20, continuous
D36V21, continuous
D36V22, continuous
D36V23, continuous
D36V24, continuous
D36V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  20P GAIN MUTATED                                     0
  20P GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  20P GAIN MUTATED                                     1
  20P GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  20P GAIN MUTATED                        10                       0
  20P GAIN WILD-TYPE                      26                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20P GAIN MUTATED                         3
  20P GAIN WILD-TYPE                       5
D36V26, multiclass
                                     clus
vv                                    20P GAIN MUTATED 20P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                           10                 26
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  20P GAIN MUTATED                                               1
  20P GAIN WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  20P GAIN MUTATED                                               10
  20P GAIN WILD-TYPE                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20P GAIN MUTATED                                                                                  30
  20P GAIN WILD-TYPE                                                                                52
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20P GAIN MUTATED                                                                                             37
  20P GAIN WILD-TYPE                                                                                           84
D36V27, multiclass
                                                                                              clus
vv                                                                                             20P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          30
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               37
                                                                                              clus
vv                                                                                             20P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            52
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V28, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   21 25
  20P GAIN WILD-TYPE 50 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     21   25
  20P GAIN WILD-TYPE   50   49
         clus
vv        20P GAIN MUTATED 20P GAIN WILD-TYPE
  ABSENT                21                 50
  PRESENT               25                 49
[1] 2 2
[1] FALSE
D36V29, continuous
D36V30, continuous
D36V31, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   13 37
  20P GAIN WILD-TYPE 36 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     13   37
  20P GAIN WILD-TYPE   36   80
                                          clus
vv                                         20P GAIN MUTATED 20P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   13                 36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               37                 80
[1] 2 2
[1] FALSE
D36V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20P GAIN MUTATED              4          20         28
  20P GAIN WILD-TYPE           11          34         57
D36V33, multiclass
              clus
vv             20P GAIN MUTATED 20P GAIN WILD-TYPE
  CURRENT USER                4                 11
  FORMER USER                20                 34
  NEVER USED                 28                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V34, continuous
D36V35, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   29  5
  20P GAIN WILD-TYPE 63 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     29    5
  20P GAIN WILD-TYPE   63   13
         clus
vv        20P GAIN MUTATED 20P GAIN WILD-TYPE
  ABSENT                29                 63
  PRESENT                5                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  20P GAIN MUTATED             0        38     1
  20P GAIN WILD-TYPE           5        62     1
D36V36, multiclass
             clus
vv            20P GAIN MUTATED 20P GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 38                 62
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V37, continuous
D36V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  20P GAIN MUTATED         2        0         0         0       11        23
  20P GAIN WILD-TYPE       3        1         1         1       23        54
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  20P GAIN MUTATED           9        2         2          2          2
  20P GAIN WILD-TYPE        28        2         6          3          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  20P GAIN MUTATED          16         1          2         17         4
  20P GAIN WILD-TYPE        28         0          1         25         3
                    vv
clus                 STAGE IVB
  20P GAIN MUTATED           3
  20P GAIN WILD-TYPE         9
D36V39, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                 11                 23
  STAGE IB1                23                 54
  STAGE IB2                 9                 28
  STAGE II                  2                  2
  STAGE IIA                 2                  6
  STAGE IIA1                2                  3
  STAGE IIA2                2                  5
  STAGE IIB                16                 28
  STAGE III                 1                  0
  STAGE IIIA                2                  1
  STAGE IIIB               17                 25
  STAGE IVA                 4                  3
  STAGE IVB                 3                  9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    86  24
  20Q GAIN WILD-TYPE 125  43
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               110                168 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                24                 43 
$`20Q GAIN MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1M6 TCGA-C5-A1M9 
       49.48        57.04       144.16       173.29        31.40        35.01 
TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       57.73        35.61         0.46         2.43        40.93         3.58 
TCGA-C5-A2LT TCGA-C5-A2LZ TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7UC 
       73.18       100.14       210.67       154.32        20.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-C5-A8XJ TCGA-C5-A8YR TCGA-DG-A2KH TCGA-DG-A2KJ 
      131.11         2.73       146.86        27.52         1.12        95.11 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT 
       82.06        63.98        22.98        17.52        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5FO 
       37.35        30.90        31.53        31.73        14.89        26.79 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       27.22        24.00         0.36        12.59        60.72        26.27 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A3GK 
        1.51         0.59         0.36         0.13        40.96         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY 
        0.76         0.03         1.22        23.84        16.11        31.36 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3L7 
       20.98        14.01        17.75        21.67        20.78       147.39 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3PZ TCGA-JX-A3Q0 
       96.95        78.71        20.48        28.37        21.11       209.59 
TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA 
       12.49        13.35        19.56        11.38        17.23         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P 
       15.58        16.41        15.95         9.04        17.56        15.88 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC 
       22.62        14.60        93.99        12.16        69.50        46.52 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM 
       23.97        19.96        36.13        11.51        39.78        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A959 
       40.87        16.64        40.14        15.68        56.35        51.32 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UT 
       24.30        46.92        45.11        27.25        47.47        15.85 
TCGA-VS-A9UU TCGA-VS-A9UZ TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-WL-A834 TCGA-ZJ-AAX4 
       14.53        67.20        17.75         4.34        26.01         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
        1.41         0.16 

$`20Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       17.52        17.82        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
       36.56       177.04        82.85         5.46        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1ML TCGA-C5-A2LS 
       46.32        30.21        53.16        38.99        20.91        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.45        83.05        78.35        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       18.02        17.85        20.42       101.82       134.33        15.48 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC 
      147.35       155.77        94.95         9.34        13.61        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ 
       45.83         8.35        99.91        23.51        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KL TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       14.73        44.94        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3HT 
       69.96        95.67        16.83        16.18         8.28        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       13.05        25.02        36.89        26.40        24.56        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        0.30        24.82         7.46        25.91        27.29        27.25 
TCGA-EA-A78R TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R8 
       13.48         6.64        19.27         0.39         0.43         1.45 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ 
        4.31         0.10         0.43        47.77         0.53         0.10 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92        15.22        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A2QG TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       15.55        19.04        36.26        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC 
       28.31        35.44        10.55         1.12        25.41        16.57 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI 
       14.93         9.44       137.16        66.81       129.37        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       15.58         8.28        18.15        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.89         0.30         0.82        22.52        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.35         8.52        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R 
       35.05        20.84        16.14        14.07         9.34        18.64 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL 
       19.59        11.67        10.03        45.57        32.42        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       32.15        53.59        59.18         4.73        33.37        58.45 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       55.50        50.14        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UQ 
       29.95        27.12         1.71        14.53        47.87        41.52 
TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
       26.07         3.42        18.25        18.84         5.16        18.25 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZX-AA5X 
       16.24        15.42        29.26        67.59        19.13         3.91 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.03               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            210.67             177.04 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            23.905             21.980 
[1] "0.0 - 210.7 (23.9)" "0.1 - 177.0 (22.0)"
[1] "hr=" "1.3"
D37V2, continuous
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED   49 23 13  4
  20Q GAIN WILD-TYPE 86 47  8  4
D37V3, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               49                 86
  T2               23                 47
  T3               13                  8
  T4                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   46 23
  20Q GAIN WILD-TYPE 83 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     46   23
  20Q GAIN WILD-TYPE   83   33
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               46                 83
  1               23                 33
[1] 2 2
[1] FALSE
D37V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   43  3
  20Q GAIN WILD-TYPE 65  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     43    3
  20Q GAIN WILD-TYPE   65    7
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               43                 65
  1                3                  7
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   18 50
  20Q GAIN WILD-TYPE 37 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     18   50
  20Q GAIN WILD-TYPE   37   73
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                18                 37
  YES               50                 73
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED               2                               90
  20Q GAIN WILD-TYPE             4                              152
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20Q GAIN MUTATED                                               3
  20Q GAIN WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20Q GAIN MUTATED                                    10
  20Q GAIN WILD-TYPE                                  11
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20Q GAIN MUTATED                                           2
  20Q GAIN WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20Q GAIN MUTATED                                              8
  20Q GAIN WILD-TYPE                                            9
D37V7, multiclass
                                               clus
vv                                              20Q GAIN MUTATED
  ADENOSQUAMOUS                                                2
  CERVICAL SQUAMOUS CELL CARCINOMA                            90
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 8
                                               clus
vv                                              20Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             152
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, continuous
D37V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     7
  20Q GAIN WILD-TYPE                                8    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED                          13
  20Q GAIN WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           0    78
  20Q GAIN WILD-TYPE                                         2   124
D37V10, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    7                 12
  BLACK OR AFRICAN AMERICAN                               13                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   78                124
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    6 63
  20Q GAIN WILD-TYPE 17 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6   63
  20Q GAIN WILD-TYPE   17   99
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 17
  NOT HISPANIC OR LATINO               63                 99
[1] 2 2
[1] FALSE
D37V12, continuous
D37V13, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    73  26
  20Q GAIN WILD-TYPE 110  48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     73   26
  20Q GAIN WILD-TYPE  110   48
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  TUMOR FREE               73                110
  WITH TUMOR               26                 48
[1] 2 2
[1] FALSE
                    vv
clus                 G1 G2 G3 G4 GX
  20Q GAIN MUTATED    6 46 50  1 11
  20Q GAIN WILD-TYPE 12 83 65  0 13
D37V14, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  G1                6                 12
  G2               46                 83
  G3               50                 65
  G4                1                  0
  GX               11                 13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, continuous
D37V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20Q GAIN MUTATED                                            19
  20Q GAIN WILD-TYPE                                          19
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  20Q GAIN MUTATED                                        3
  20Q GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  20Q GAIN MUTATED                                                 1
  20Q GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20Q GAIN MUTATED               19                  56
  20Q GAIN WILD-TYPE             43                  87
D37V17, multiclass
                                                 clus
vv                                                20Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                19
  LIFELONG NON-SMOKER                                           56
                                                 clus
vv                                                20Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  43
  LIFELONG NON-SMOKER                                             87
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V18, continuous
D37V19, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    9  2
  20Q GAIN WILD-TYPE 16  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      9    2
  20Q GAIN WILD-TYPE   16    1
                         clus
vv                        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                2                  1
[1] 2 2
[1] FALSE
D37V20, continuous
D37V21, continuous
D37V22, continuous
D37V23, continuous
D37V24, continuous
D37V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  20Q GAIN MUTATED                                     0
  20Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  20Q GAIN MUTATED                                     1
  20Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  20Q GAIN MUTATED                        11                       0
  20Q GAIN WILD-TYPE                      25                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20Q GAIN MUTATED                         4
  20Q GAIN WILD-TYPE                       4
D37V26, multiclass
                                     clus
vv                                    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                           11                 25
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            4                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  20Q GAIN MUTATED                                               0
  20Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  20Q GAIN MUTATED                                               11
  20Q GAIN WILD-TYPE                                             14
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20Q GAIN MUTATED                                                                                  34
  20Q GAIN WILD-TYPE                                                                                48
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20Q GAIN MUTATED                                                                                             43
  20Q GAIN WILD-TYPE                                                                                           78
D37V27, multiclass
                                                                                              clus
vv                                                                                             20Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          34
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               43
                                                                                              clus
vv                                                                                             20Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V28, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   29 27
  20Q GAIN WILD-TYPE 42 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     29   27
  20Q GAIN WILD-TYPE   42   47
         clus
vv        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ABSENT                29                 42
  PRESENT               27                 47
[1] 2 2
[1] FALSE
D37V29, continuous
D37V30, continuous
D37V31, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   13 43
  20Q GAIN WILD-TYPE 36 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     13   43
  20Q GAIN WILD-TYPE   36   74
                                          clus
vv                                         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   13                 36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               43                 74
[1] 2 2
[1] FALSE
D37V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20Q GAIN MUTATED              5          23         31
  20Q GAIN WILD-TYPE           10          31         54
D37V33, multiclass
              clus
vv             20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CURRENT USER                5                 10
  FORMER USER                23                 31
  NEVER USED                 31                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V34, continuous
D37V35, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   36  6
  20Q GAIN WILD-TYPE 56 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     36    6
  20Q GAIN WILD-TYPE   56   12
         clus
vv        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ABSENT                36                 56
  PRESENT                6                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  20Q GAIN MUTATED             1        40     2
  20Q GAIN WILD-TYPE           4        60     0
D37V36, multiclass
             clus
vv            20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 40                 60
  OTHER                      2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V37, continuous
D37V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  20Q GAIN MUTATED         2        0         0         0       13        29
  20Q GAIN WILD-TYPE       3        1         1         1       21        48
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  20Q GAIN MUTATED           9        4         3          3          2
  20Q GAIN WILD-TYPE        28        0         5          2          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  20Q GAIN MUTATED          17         1          2         19         4
  20Q GAIN WILD-TYPE        27         0          1         23         3
                    vv
clus                 STAGE IVB
  20Q GAIN MUTATED           3
  20Q GAIN WILD-TYPE         9
D37V39, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                 13                 21
  STAGE IB1                29                 48
  STAGE IB2                 9                 28
  STAGE II                  4                  0
  STAGE IIA                 3                  5
  STAGE IIA1                3                  2
  STAGE IIA2                2                  5
  STAGE IIB                17                 27
  STAGE III                 1                  0
  STAGE IIIA                2                  1
  STAGE IIIB               19                 23
  STAGE IVA                 4                  3
  STAGE IVB                 3                  9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    25   9
  21Q GAIN WILD-TYPE 186  58
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                244 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 9                 58 
$`21Q GAIN MUTATED`
TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MP 
       19.86        31.40        38.99        35.61         2.43         3.58 
TCGA-C5-A2LZ TCGA-C5-A7X8 TCGA-DG-A2KH TCGA-DG-A2KL TCGA-EA-A1QS TCGA-EA-A3HQ 
      100.14         2.73         1.12        44.94        39.55        37.35 
TCGA-EA-A5O9 TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2RA TCGA-EK-A2RK TCGA-FU-A3TX 
       25.91        19.27         0.59        40.96         0.43         1.48 
TCGA-HM-A3JK TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AU 
       20.78        36.36        21.44        21.11        44.61        11.28 
TCGA-LP-A5U2 TCGA-MY-A5BE TCGA-MY-A913 TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A8QF 
        0.30        35.05        17.23        19.96        36.13        59.18 
TCGA-VS-A9UI TCGA-VS-A9UU TCGA-VS-A9V3 TCGA-ZJ-AAXA 
       45.11        14.53        17.75         1.41 

$`21Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       82.85         5.46        67.46        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS 
       57.73        53.16         0.46        20.91        40.93        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.18        73.45        83.05        78.35        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       52.01        18.02        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC 
      155.77       131.11        94.95         9.34        13.61        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       45.83         8.35       146.86        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KM 
       20.81        20.91        14.73        95.11        82.06        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76        55.63        69.96        95.67 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT 
       22.98        16.83        16.18        17.52         8.28        40.87 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        31.73        26.01         0.30        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
        7.46        14.89        26.79        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       24.00        13.48         0.36        12.59        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64         1.51         0.39         0.43         0.36         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ 
        0.13         4.31         0.10        47.77         0.53         0.10 
TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.49         0.76         0.03        20.35         7.92        15.22 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         8.32        15.55         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 
       17.75        25.41        16.57        21.67        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VK 
       81.96        29.85        27.42         3.29        24.56        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A5QV 
       15.58        28.37         8.28        18.15       209.59        20.91 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
        0.89        12.49         0.82        13.35        22.52        19.56 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         8.35         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
       34.62        19.96        54.81        20.84         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        69.50        10.03        46.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       45.57        32.42        23.97        65.49        32.15        53.59 
TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       33.37        40.14        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL 
       29.95        27.12        24.30        46.92         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
        4.34        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         0.16         3.91 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.30               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            100.14             210.67 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            20.945             23.755 
[1] "0.3 - 100.1 (20.9)" "0.0 - 210.7 (23.8)"
[1] "hr=" "1.4"
D38V2, continuous
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED    13  12   1   1
  21Q GAIN WILD-TYPE 122  58  20   7
D38V3, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               13                122
  T2               12                 58
  T3                1                 20
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    16   7
  21Q GAIN WILD-TYPE 113  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     16    7
  21Q GAIN WILD-TYPE  113   49
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               16                113
  1                7                 49
[1] 2 2
[1] FALSE
D38V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   13  2
  21Q GAIN WILD-TYPE 95  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     13    2
  21Q GAIN WILD-TYPE   95    8
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               13                 95
  1                2                  8
[1] 2 2
[1] FALSE
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     7  14
  21Q GAIN WILD-TYPE  48 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7   14
  21Q GAIN WILD-TYPE   48  109
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 7                 48
  YES               14                109
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED               1                               33
  21Q GAIN WILD-TYPE             5                              209
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  21Q GAIN MUTATED                                               1
  21Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  21Q GAIN MUTATED                                     1
  21Q GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  21Q GAIN MUTATED                                           0
  21Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  21Q GAIN MUTATED                                              1
  21Q GAIN WILD-TYPE                                           16
D38V7, multiclass
                                               clus
vv                                              21Q GAIN MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            33
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              21Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             209
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, continuous
D38V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1     3
  21Q GAIN WILD-TYPE                                7    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED                           3
  21Q GAIN WILD-TYPE                        25
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           0    22
  21Q GAIN WILD-TYPE                                         2   180
D38V10, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                3                 25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   22                180
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3  18
  21Q GAIN WILD-TYPE  20 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3   18
  21Q GAIN WILD-TYPE   20  144
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 20
  NOT HISPANIC OR LATINO               18                144
[1] 2 2
[1] FALSE
D38V12, continuous
D38V13, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    18  13
  21Q GAIN WILD-TYPE 165  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     18   13
  21Q GAIN WILD-TYPE  165   61
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  TUMOR FREE               18                165
  WITH TUMOR               13                 61
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  21Q GAIN MUTATED     2  12  19   0   3
  21Q GAIN WILD-TYPE  16 117  96   1  21
D38V14, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  G1                2                 16
  G2               12                117
  G3               19                 96
  G4                0                  1
  GX                3                 21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V15, continuous
D38V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  21Q GAIN MUTATED                                             6
  21Q GAIN WILD-TYPE                                          32
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  21Q GAIN MUTATED                                        2
  21Q GAIN WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  21Q GAIN MUTATED                                                 1
  21Q GAIN WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  21Q GAIN MUTATED                5                  17
  21Q GAIN WILD-TYPE             57                 126
D38V17, multiclass
                                                 clus
vv                                                21Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 5
  LIFELONG NON-SMOKER                                           17
                                                 clus
vv                                                21Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  57
  LIFELONG NON-SMOKER                                            126
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V18, continuous
D38V19, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  1
  21Q GAIN WILD-TYPE 22  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    1
  21Q GAIN WILD-TYPE   22    2
                         clus
vv                        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   3                 22
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D38V20, continuous
D38V21, continuous
D38V22, continuous
D38V23, continuous
D38V24, continuous
D38V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  21Q GAIN MUTATED                                     0
  21Q GAIN WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  21Q GAIN MUTATED                                     0
  21Q GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  21Q GAIN MUTATED                         2                       0
  21Q GAIN WILD-TYPE                      34                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  21Q GAIN MUTATED                         2
  21Q GAIN WILD-TYPE                       6
D38V26, multiclass
                                     clus
vv                                    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            2                 34
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  21Q GAIN MUTATED                                               0
  21Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  21Q GAIN MUTATED                                                2
  21Q GAIN WILD-TYPE                                             23
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  21Q GAIN MUTATED                                                                                  17
  21Q GAIN WILD-TYPE                                                                                65
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  21Q GAIN MUTATED                                                                                             10
  21Q GAIN WILD-TYPE                                                                                          111
D38V27, multiclass
                                                                                              clus
vv                                                                                             21Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               10
                                                                                              clus
vv                                                                                             21Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V28, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   10  8
  21Q GAIN WILD-TYPE 61 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    8
  21Q GAIN WILD-TYPE   61   66
         clus
vv        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ABSENT                10                 61
  PRESENT                8                 66
[1] 2 2
[1] FALSE
D38V29, continuous
D38V30, continuous
D38V31, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     9   8
  21Q GAIN WILD-TYPE  40 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9    8
  21Q GAIN WILD-TYPE   40  109
                                          clus
vv                                         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                8                109
[1] 2 2
[1] FALSE
D38V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  21Q GAIN MUTATED              1           3          8
  21Q GAIN WILD-TYPE           14          51         77
D38V33, multiclass
              clus
vv             21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 3                 51
  NEVER USED                  8                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V34, continuous
D38V35, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   10  1
  21Q GAIN WILD-TYPE 82 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    1
  21Q GAIN WILD-TYPE   82   17
         clus
vv        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ABSENT                10                 82
  PRESENT                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  21Q GAIN MUTATED             1        11     0
  21Q GAIN WILD-TYPE           4        89     2
D38V36, multiclass
             clus
vv            21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 11                 89
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V37, continuous
D38V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  21Q GAIN MUTATED         0        0         0         1        2         9
  21Q GAIN WILD-TYPE       5        1         1         0       32        68
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  21Q GAIN MUTATED           3        1         2          0          2
  21Q GAIN WILD-TYPE        34        3         6          5          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  21Q GAIN MUTATED           8         0          0          8         0
  21Q GAIN WILD-TYPE        36         1          3         34         7
                    vv
clus                 STAGE IVB
  21Q GAIN MUTATED           1
  21Q GAIN WILD-TYPE        11
D38V39, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  2                 32
  STAGE IB1                 9                 68
  STAGE IB2                 3                 34
  STAGE II                  1                  3
  STAGE IIA                 2                  6
  STAGE IIA1                0                  5
  STAGE IIA2                2                  5
  STAGE IIB                 8                 36
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB                8                 34
  STAGE IVA                 0                  7
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    22   5
  22Q GAIN WILD-TYPE 189  62
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                27                251 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 62 
$`22Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BJ TCGA-C5-A1ML TCGA-C5-A2LY TCGA-C5-A7CG TCGA-C5-A7CH 
       57.04       144.16        20.91        78.35       210.67       154.32 
TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A8YQ TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A5ZF 
       17.19       131.11        23.51        22.98        39.55        27.22 
TCGA-EK-A2PI TCGA-EK-A2R9 TCGA-FU-A3NI TCGA-FU-A40J TCGA-JW-A5VI TCGA-JX-A3Q8 
       19.27         0.13        20.98        14.01        24.56        44.61 
TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-MU-A51Y TCGA-MY-A5BE TCGA-PN-A8MA TCGA-VS-A8QF 
       11.28         0.30        28.08        35.05         2.96        59.18 
TCGA-VS-A9UD TCGA-VS-A9UP TCGA-VS-A9UV 
       24.30        47.47         3.42 

$`22Q GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       18.74        36.56       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
       19.86        67.46        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       57.73        53.16        38.99        35.61         0.46         2.43 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       40.93         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       20.42       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      155.77        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83         8.35       146.86        99.91        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91        14.73         1.12        95.11        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       63.98        87.75        58.88        36.76        55.63        69.96 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT 
       95.67        16.83        16.18        17.52         8.28        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01         0.30 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       27.25        24.00        13.48         0.36        12.59        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
       26.27         6.64         1.51         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK 
        0.36         1.45        40.96         4.31         0.10         0.43 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN 
       47.77         0.53         0.10         0.49         0.76         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92        15.22        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       15.55         1.22        23.84        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
       36.26        26.14         1.48        16.14        28.31        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       10.55         1.12        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AW 
        8.28        18.15        21.11       209.59        20.91         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
       12.49         0.82        13.35        22.52        19.56        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         8.35         8.52        11.38        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       54.81        20.84        17.23        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       23.97        19.96        65.49        32.15        53.59        36.13 
TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       33.37        40.14        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       29.95        27.12        46.92        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       27.25        47.87        41.52        26.07        15.85        14.53 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
        4.34        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         1.41         0.16         3.91 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.13               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            210.67             209.59 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             24.56              21.67 
[1] "0.1 - 210.7 (24.6)" "0.0 - 209.6 (21.7)"
[1] "hr=" "1.7"
D39V2, continuous
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED    10   7   2   1
  22Q GAIN WILD-TYPE 125  63  19   7
D39V3, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               10                125
  T2                7                 63
  T3                2                 19
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    10   5
  22Q GAIN WILD-TYPE 119  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10    5
  22Q GAIN WILD-TYPE  119   51
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               10                119
  1                5                 51
[1] 2 2
[1] FALSE
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     8   0
  22Q GAIN WILD-TYPE 100  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      8    0
  22Q GAIN WILD-TYPE  100   10
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                8                100
  1                0                 10
[1] 2 2
[1] FALSE
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    10   9
  22Q GAIN WILD-TYPE  45 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10    9
  22Q GAIN WILD-TYPE   45  114
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                10                 45
  YES                9                114
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED               0                               25
  22Q GAIN WILD-TYPE             6                              217
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  22Q GAIN MUTATED                                               1
  22Q GAIN WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  22Q GAIN MUTATED                                     2
  22Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  22Q GAIN MUTATED                                           0
  22Q GAIN WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  22Q GAIN MUTATED                                              1
  22Q GAIN WILD-TYPE                                           16
D39V7, multiclass
                                               clus
vv                                              22Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            25
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              22Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             217
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, continuous
D39V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  2     4
  22Q GAIN WILD-TYPE                                6    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED                           2
  22Q GAIN WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    18
  22Q GAIN WILD-TYPE                                         2   184
D39V10, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                                2                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   18                184
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     2  17
  22Q GAIN WILD-TYPE  21 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   17
  22Q GAIN WILD-TYPE   21  145
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 21
  NOT HISPANIC OR LATINO               17                145
[1] 2 2
[1] FALSE
D39V12, continuous
D39V13, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    18  10
  22Q GAIN WILD-TYPE 165  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     18   10
  22Q GAIN WILD-TYPE  165   64
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  TUMOR FREE               18                165
  WITH TUMOR               10                 64
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  22Q GAIN MUTATED     1  12  15   0   1
  22Q GAIN WILD-TYPE  17 117 100   1  23
D39V14, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  G1                1                 17
  G2               12                117
  G3               15                100
  G4                0                  1
  GX                1                 23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, continuous
D39V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  22Q GAIN MUTATED                                             2
  22Q GAIN WILD-TYPE                                          36
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  22Q GAIN MUTATED                                        1
  22Q GAIN WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  22Q GAIN MUTATED                                                 0
  22Q GAIN WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  22Q GAIN MUTATED                6                  14
  22Q GAIN WILD-TYPE             56                 129
D39V17, multiclass
                                                 clus
vv                                                22Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 6
  LIFELONG NON-SMOKER                                           14
                                                 clus
vv                                                22Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  56
  LIFELONG NON-SMOKER                                            129
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V18, continuous
D39V19, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  0
  22Q GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    0
  22Q GAIN WILD-TYPE   21    3
                         clus
vv                        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D39V20, continuous
D39V21, continuous
D39V22, continuous
D39V23, continuous
D39V24, continuous
D39V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  22Q GAIN MUTATED                                     1
  22Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  22Q GAIN MUTATED                                     0
  22Q GAIN WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  22Q GAIN MUTATED                         4                       0
  22Q GAIN WILD-TYPE                      32                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  22Q GAIN MUTATED                         0
  22Q GAIN WILD-TYPE                       8
D39V26, multiclass
                                     clus
vv                                    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                1                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            4                 32
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  22Q GAIN MUTATED                                               0
  22Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  22Q GAIN MUTATED                                                2
  22Q GAIN WILD-TYPE                                             23
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  22Q GAIN MUTATED                                                                                   7
  22Q GAIN WILD-TYPE                                                                                75
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  22Q GAIN MUTATED                                                                                             13
  22Q GAIN WILD-TYPE                                                                                          108
D39V27, multiclass
                                                                                              clus
vv                                                                                             22Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               13
                                                                                              clus
vv                                                                                             22Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            75
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V28, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    6  6
  22Q GAIN WILD-TYPE 65 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      6    6
  22Q GAIN WILD-TYPE   65   68
         clus
vv        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ABSENT                 6                 65
  PRESENT                6                 68
[1] 2 2
[1] FALSE
D39V29, continuous
D39V30, continuous
D39V31, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     5   9
  22Q GAIN WILD-TYPE  44 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5    9
  22Q GAIN WILD-TYPE   44  108
                                          clus
vv                                         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    5                 44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                9                108
[1] 2 2
[1] FALSE
D39V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  22Q GAIN MUTATED              0           7          6
  22Q GAIN WILD-TYPE           15          47         79
D39V33, multiclass
              clus
vv             22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CURRENT USER                0                 15
  FORMER USER                 7                 47
  NEVER USED                  6                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V34, continuous
D39V35, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    7  0
  22Q GAIN WILD-TYPE 85 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      7    0
  22Q GAIN WILD-TYPE   85   18
         clus
vv        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ABSENT                 7                 85
  PRESENT                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  22Q GAIN MUTATED             0         9     0
  22Q GAIN WILD-TYPE           5        91     2
D39V36, multiclass
             clus
vv            22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                  9                 91
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V37, continuous
D39V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  22Q GAIN MUTATED         0        0         0         0        4         8
  22Q GAIN WILD-TYPE       5        1         1         1       30        69
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  22Q GAIN MUTATED           1        0         1          1          0
  22Q GAIN WILD-TYPE        36        4         7          4          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  22Q GAIN MUTATED           6         0          1          6         1
  22Q GAIN WILD-TYPE        38         1          2         36         6
                    vv
clus                 STAGE IVB
  22Q GAIN MUTATED           0
  22Q GAIN WILD-TYPE        12
D39V39, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  4                 30
  STAGE IB1                 8                 69
  STAGE IB2                 1                 36
  STAGE II                  0                  4
  STAGE IIA                 1                  7
  STAGE IIA1                1                  4
  STAGE IIA2                0                  7
  STAGE IIB                 6                 38
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                6                 36
  STAGE IVA                 1                  6
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    28  13
  XP GAIN WILD-TYPE 183  54
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               41               237 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               13                54 
$`XP GAIN MUTATED`
TCGA-4J-AA1J TCGA-C5-A1BK TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1ME 
       17.82       177.04        19.86        67.46        46.32        57.73 
TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LX TCGA-C5-A7CH TCGA-C5-A7CO TCGA-C5-A7X5 
        2.43         3.58        83.05       154.32       147.35        13.61 
TCGA-C5-A8XI TCGA-DS-A0VK TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3QD TCGA-EA-A5O9 
        8.35        36.76        22.98         8.28        13.05        25.91 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EX-A69M TCGA-IR-A3LL TCGA-JW-A5VL TCGA-JW-A852 
       27.25        27.22         8.32        36.36        15.58         8.28 
TCGA-JX-A3Q0 TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA41 TCGA-Q1-A5R3 TCGA-Q1-A73Q 
      209.59         0.30         0.82         8.35        15.95         9.34 
TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QA TCGA-VS-A94X TCGA-VS-A953 
       10.03        23.97        19.96        36.13        16.64        15.68 
TCGA-VS-A954 TCGA-VS-A9U6 TCGA-VS-A9UB TCGA-VS-A9V1 TCGA-ZJ-AAXA 
       56.35        43.40        29.95         5.16         1.41 

$`XP GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       18.74        36.56       144.16       173.29        82.85         5.46 
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       31.40        30.21        35.01        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        0.46        20.91        40.93        44.22        73.18        73.45 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35        17.19       155.77       131.11        94.95         9.34 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
        2.73        50.99        45.83       146.86        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52        20.81        20.91        14.73         1.12        95.11 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       82.06        44.94        63.98        87.75        58.88        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS 
       69.96        95.67        16.83        16.18        17.52        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
       40.87        37.35        30.90        31.53        31.36        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01         0.30 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A6QX 
       24.82         7.46        14.89        26.79        27.29        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       13.48         0.36        12.59        60.72        26.27         6.64 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        1.51        19.27         0.39         0.43         0.59         0.36 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK 
        1.45         0.13        40.96         4.31         0.10         0.43 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN 
       47.77         0.53         0.10         0.49         0.76         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF 
       20.35         7.92        15.22        14.70        19.79        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       20.98        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       35.44        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       129.37        96.95        78.71        81.96        29.85 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        20.48        28.37 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       18.15        21.11        44.61        20.91        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
       12.49        13.35        22.52        19.56        17.82        19.56 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       35.05        20.84        17.23         2.96        15.58        16.41 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R 
        9.04        16.14        17.56        14.07        15.88        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       22.62        19.59        14.60        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 
       69.50        46.52        45.57        32.42        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       53.59        11.51        59.18        39.78        31.27        40.87 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A957 TCGA-VS-A958 
        4.73        33.37        40.14        58.45        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UD 
       51.32        50.47        48.39        28.50        27.12        24.30 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       46.92        45.11         1.71        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       18.25        67.20        18.84        18.25        17.75         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         0.16         3.91 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.30              0.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           209.59            210.67 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            19.86             23.84 
[1] "0.3 - 209.6 (19.9)" "0.0 - 210.7 (23.8)"
[1] "hr=" "1.4"
D40V2, continuous
                   vv
clus                 T1  T2  T3  T4
  XP GAIN MUTATED    18   8   7   2
  XP GAIN WILD-TYPE 117  62  14   6
D40V3, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              18               117
  T2               8                62
  T3               7                14
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    16   9
  XP GAIN WILD-TYPE 113  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     16    9
  XP GAIN WILD-TYPE  113   47
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              16               113
  1               9                47
[1] 2 2
[1] FALSE
D40V5, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   15  4
  XP GAIN WILD-TYPE 93  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     15    4
  XP GAIN WILD-TYPE   93    6
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              15                93
  1               4                 6
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    8 24
  XP GAIN WILD-TYPE 47 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      8   24
  XP GAIN WILD-TYPE   47   99
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                8                47
  YES              24                99
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  XP GAIN MUTATED               0                               39
  XP GAIN WILD-TYPE             6                              203
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  XP GAIN MUTATED                                               1
  XP GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  XP GAIN MUTATED                                     1
  XP GAIN WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  XP GAIN MUTATED                                           0
  XP GAIN WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  XP GAIN MUTATED                                              1
  XP GAIN WILD-TYPE                                           16
D40V7, multiclass
                                               clus
vv                                              XP GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           39
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              XP GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            203
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, continuous
D40V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  1     4
  XP GAIN WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XP GAIN MUTATED                           6
  XP GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP GAIN MUTATED                                           0    25
  XP GAIN WILD-TYPE                                         2   177
D40V10, multiclass
                                           clus
vv                                          XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                               6                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  25               177
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     3  24
  XP GAIN WILD-TYPE  20 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3   24
  XP GAIN WILD-TYPE   20  138
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                20
  NOT HISPANIC OR LATINO              24               138
[1] 2 2
[1] FALSE
D40V12, continuous
D40V13, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    25  15
  XP GAIN WILD-TYPE 158  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     25   15
  XP GAIN WILD-TYPE  158   59
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  TUMOR FREE              25               158
  WITH TUMOR              15                59
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  XP GAIN MUTATED     2  20  14   0   6
  XP GAIN WILD-TYPE  16 109 101   1  18
D40V14, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  G1               2                16
  G2              20               109
  G3              14               101
  G4               0                 1
  GX               6                18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V15, continuous
D40V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  XP GAIN MUTATED                                             5
  XP GAIN WILD-TYPE                                          33
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  XP GAIN MUTATED                                        3
  XP GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  XP GAIN MUTATED                                                 0
  XP GAIN WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  XP GAIN MUTATED                7                  25
  XP GAIN WILD-TYPE             55                 118
D40V17, multiclass
                                                 clus
vv                                                XP GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                7
  LIFELONG NON-SMOKER                                          25
                                                 clus
vv                                                XP GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 55
  LIFELONG NON-SMOKER                                           118
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V18, continuous
D40V19, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    2  1
  XP GAIN WILD-TYPE 23  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      2    1
  XP GAIN WILD-TYPE   23    2
                         clus
vv                        XP GAIN MUTATED XP GAIN WILD-TYPE
  COMPLETED AS PLANNED                  2                23
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D40V20, continuous
D40V21, continuous
D40V22, continuous
D40V23, continuous
D40V24, continuous
D40V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  XP GAIN MUTATED                                     0
  XP GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  XP GAIN MUTATED                                     0                       7
  XP GAIN WILD-TYPE                                   7                      29
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  XP GAIN MUTATED                         0                       3
  XP GAIN WILD-TYPE                       1                       5
D40V26, multiclass
                                     clus
vv                                    XP GAIN MUTATED XP GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           7                29
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           3                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  XP GAIN MUTATED                                               1
  XP GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  XP GAIN MUTATED                                                3
  XP GAIN WILD-TYPE                                             22
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  XP GAIN MUTATED                                                                                  14
  XP GAIN WILD-TYPE                                                                                68
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  XP GAIN MUTATED                                                                                             19
  XP GAIN WILD-TYPE                                                                                          102
D40V27, multiclass
                                                                                              clus
vv                                                                                             XP GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              19
                                                                                              clus
vv                                                                                             XP GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V28, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    7 10
  XP GAIN WILD-TYPE 64 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      7   10
  XP GAIN WILD-TYPE   64   64
         clus
vv        XP GAIN MUTATED XP GAIN WILD-TYPE
  ABSENT                7                64
  PRESENT              10                64
[1] 2 2
[1] FALSE
D40V29, continuous
D40V30, continuous
D40V31, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   10 18
  XP GAIN WILD-TYPE 39 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     10   18
  XP GAIN WILD-TYPE   39   99
                                          clus
vv                                         XP GAIN MUTATED XP GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  10                39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              18                99
[1] 2 2
[1] FALSE
D40V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  XP GAIN MUTATED              0           8         16
  XP GAIN WILD-TYPE           15          46         69
D40V33, multiclass
              clus
vv             XP GAIN MUTATED XP GAIN WILD-TYPE
  CURRENT USER               0                15
  FORMER USER                8                46
  NEVER USED                16                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V34, continuous
D40V35, binary
                   cls
clus                 0  1
  XP GAIN MUTATED   13  0
  XP GAIN WILD-TYPE 79 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     13    0
  XP GAIN WILD-TYPE   79   18
         clus
vv        XP GAIN MUTATED XP GAIN WILD-TYPE
  ABSENT               13                79
  PRESENT               0                18
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  XP GAIN MUTATED             2        18     0
  XP GAIN WILD-TYPE           3        82     2
D40V36, multiclass
             clus
vv            XP GAIN MUTATED XP GAIN WILD-TYPE
  CARBOPLATIN               2                 3
  CISPLATIN                18                82
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V37, continuous
[1] "Remove cluster labels:" "XP GAIN MUTATED"       
clus
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                2                15 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JX-A3Q8 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42        TCGA-MU-A51Y 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" "XP GAIN WILD-TYPE" 
D40V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  XP GAIN MUTATED         1        0         0         0        4         8
  XP GAIN WILD-TYPE       4        1         1         1       30        69
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  XP GAIN MUTATED           7        0         0          0          1
  XP GAIN WILD-TYPE        30        4         8          5          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  XP GAIN MUTATED           7         1          0          8         1
  XP GAIN WILD-TYPE        37         0          3         34         6
                   vv
clus                STAGE IVB
  XP GAIN MUTATED           3
  XP GAIN WILD-TYPE         9
D40V39, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 4                30
  STAGE IB1                8                69
  STAGE IB2                7                30
  STAGE II                 0                 4
  STAGE IIA                0                 8
  STAGE IIA1               0                 5
  STAGE IIA2               1                 6
  STAGE IIB                7                37
  STAGE III                1                 0
  STAGE IIIA               0                 3
  STAGE IIIB               8                34
  STAGE IVA                1                 6
  STAGE IVB                3                 9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    33   7
  XQ GAIN WILD-TYPE 178  60
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               40               238 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7                60 
$`XQ GAIN MUTATED`
TCGA-4J-AA1J TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1MF 
       17.82       177.04        67.46        46.32        57.73        53.16 
TCGA-C5-A1MP TCGA-C5-A2LV TCGA-C5-A7CH TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-DS-A3LQ 
        3.58        73.45       154.32         8.35        23.51        22.98 
TCGA-EA-A3QD TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PM 
       13.05        25.91        27.22        60.72         1.51         0.59 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LL TCGA-JX-A3Q0 
       23.84        20.98       137.16        66.81        36.36       209.59 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-Q1-A5R3 TCGA-Q1-A73Q TCGA-VS-A8EB TCGA-VS-A8EI 
        0.30         0.82        15.95         9.34        10.03        23.97 
TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A94X TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A954 
       36.13        59.18        16.64        40.14        15.68        56.35 
TCGA-VS-A9UB TCGA-VS-A9UP TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
       29.95        47.47        67.59         1.41 

$`XQ GAIN WILD-TYPE`
TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        49.48        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       18.74        36.56       144.16       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI 
       19.86        31.40        30.21        35.01        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91        40.93        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       210.67       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48        20.35       147.35        17.19       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       94.95         9.34        13.61         2.73        50.99        45.83 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
      146.86        99.91        27.52        20.81        20.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        95.11        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        36.76        55.63        69.96        95.67        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       30.90        31.53        31.36        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       24.56        31.73        26.01         0.30        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
       14.89        26.79        27.29        27.25        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK 
        0.36        12.59        26.27         6.64        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC 
        0.43         0.36         1.45         0.13        40.96         4.31 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.10         0.43        47.77         0.53         0.10         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.76         0.03        20.35         7.92        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       19.79         8.32        15.55         1.22        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36        36.26        26.14         1.48        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       14.01        35.44        10.55         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       16.57        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      129.37        96.95        78.71        81.96        29.85        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        8.28        18.15        21.11        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.89        12.49        13.35        22.52        19.56        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         8.35         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
       19.96        54.81        35.05        20.84        17.23         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
       15.88        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       93.99        12.16        69.50        46.52        45.57        32.42 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QH 
       19.96        65.49        32.15        53.59        11.51        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A957 
       31.27        40.87         4.73        33.37        58.45        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       27.12        24.30        46.92        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       27.25        47.87        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       17.75         4.34        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         0.16         3.91 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.30              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           209.59            210.67 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           26.565            21.275 
[1] "0.3 - 209.6 (26.6)" "0.0 - 210.7 (21.3)"
[1] "hr=" "1.8"
D41V2, continuous
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED    20   5   7   1
  XQ GAIN WILD-TYPE 115  65  14   7
D41V3, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              20               115
  T2               5                65
  T3               7                14
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    19   6
  XQ GAIN WILD-TYPE 110  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     19    6
  XQ GAIN WILD-TYPE  110   50
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              19               110
  1               6                50
[1] 2 2
[1] FALSE
D41V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   15  1
  XQ GAIN WILD-TYPE 93  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     15    1
  XQ GAIN WILD-TYPE   93    9
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              15                93
  1               1                 9
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     4  23
  XQ GAIN WILD-TYPE  51 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4   23
  XQ GAIN WILD-TYPE   51  100
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                4                51
  YES              23               100
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED               0                               37
  XQ GAIN WILD-TYPE             6                              205
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  XQ GAIN MUTATED                                               1
  XQ GAIN WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  XQ GAIN MUTATED                                     2
  XQ GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  XQ GAIN MUTATED                                           1
  XQ GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  XQ GAIN MUTATED                                              1
  XQ GAIN WILD-TYPE                                           16
D41V7, multiclass
                                               clus
vv                                              XQ GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           37
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              XQ GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            205
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, continuous
D41V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     3
  XQ GAIN WILD-TYPE                                8    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED                           7
  XQ GAIN WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           0    24
  XQ GAIN WILD-TYPE                                         2   178
D41V10, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               7                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  24               178
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  23
  XQ GAIN WILD-TYPE  23 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   23
  XQ GAIN WILD-TYPE   23  139
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                23
  NOT HISPANIC OR LATINO              23               139
[1] 2 2
[1] FALSE
D41V12, continuous
D41V13, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    27  11
  XQ GAIN WILD-TYPE 156  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     27   11
  XQ GAIN WILD-TYPE  156   63
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  TUMOR FREE              27               156
  WITH TUMOR              11                63
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  XQ GAIN MUTATED     1  17  18   0   6
  XQ GAIN WILD-TYPE  17 112  97   1  18
D41V14, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  G1               1                17
  G2              17               112
  G3              18                97
  G4               0                 1
  GX               6                18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, continuous
D41V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  XQ GAIN MUTATED                                             4
  XQ GAIN WILD-TYPE                                          34
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  XQ GAIN MUTATED                                        3
  XQ GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  XQ GAIN MUTATED                                                 0
  XQ GAIN WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  XQ GAIN MUTATED               10                  21
  XQ GAIN WILD-TYPE             52                 122
D41V17, multiclass
                                                 clus
vv                                                XQ GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               10
  LIFELONG NON-SMOKER                                          21
                                                 clus
vv                                                XQ GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    34
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 52
  LIFELONG NON-SMOKER                                           122
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V18, continuous
D41V19, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  1
  XQ GAIN WILD-TYPE 23  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    1
  XQ GAIN WILD-TYPE   23    2
                         clus
vv                        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COMPLETED AS PLANNED                  2                23
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D41V20, continuous
D41V21, continuous
D41V22, continuous
D41V23, continuous
D41V24, continuous
D41V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  XQ GAIN MUTATED                                     0
  XQ GAIN WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  XQ GAIN MUTATED                                     0                       9
  XQ GAIN WILD-TYPE                                   7                      27
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  XQ GAIN MUTATED                         0                       1
  XQ GAIN WILD-TYPE                       1                       7
D41V26, multiclass
                                     clus
vv                                    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           9                27
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  XQ GAIN MUTATED                                               1
  XQ GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  XQ GAIN MUTATED                                                3
  XQ GAIN WILD-TYPE                                             22
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  XQ GAIN MUTATED                                                                                  15
  XQ GAIN WILD-TYPE                                                                                67
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  XQ GAIN MUTATED                                                                                             18
  XQ GAIN WILD-TYPE                                                                                          103
D41V27, multiclass
                                                                                              clus
vv                                                                                             XQ GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              18
                                                                                              clus
vv                                                                                             XQ GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           67
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V28, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    8 11
  XQ GAIN WILD-TYPE 63 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8   11
  XQ GAIN WILD-TYPE   63   63
         clus
vv        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ABSENT                8                63
  PRESENT              11                63
[1] 2 2
[1] FALSE
D41V29, continuous
D41V30, continuous
D41V31, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     8  14
  XQ GAIN WILD-TYPE  41 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8   14
  XQ GAIN WILD-TYPE   41  103
                                          clus
vv                                         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   8                41
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              14               103
[1] 2 2
[1] FALSE
D41V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  XQ GAIN MUTATED              0           6         17
  XQ GAIN WILD-TYPE           15          48         68
D41V33, multiclass
              clus
vv             XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CURRENT USER               0                15
  FORMER USER                6                48
  NEVER USED                17                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V34, continuous
D41V35, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   14  1
  XQ GAIN WILD-TYPE 78 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     14    1
  XQ GAIN WILD-TYPE   78   17
         clus
vv        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ABSENT               14                78
  PRESENT               1                17
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  XQ GAIN MUTATED             0        14     0
  XQ GAIN WILD-TYPE           5        86     2
D41V36, multiclass
             clus
vv            XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                14                86
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V37, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D41V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  XQ GAIN MUTATED         1        0         0         0        4        10
  XQ GAIN WILD-TYPE       4        1         1         1       30        67
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  XQ GAIN MUTATED           5        0         1          1          0
  XQ GAIN WILD-TYPE        32        4         7          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  XQ GAIN MUTATED           8         1          1          6         1
  XQ GAIN WILD-TYPE        36         0          2         36         6
                   vv
clus                STAGE IVB
  XQ GAIN MUTATED           1
  XQ GAIN WILD-TYPE        11
D41V39, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 4                30
  STAGE IB1               10                67
  STAGE IB2                5                32
  STAGE II                 0                 4
  STAGE IIA                1                 7
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                8                36
  STAGE III                1                 0
  STAGE IIIA               1                 2
  STAGE IIIB               6                36
  STAGE IVA                1                 6
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     9   3
  1P LOSS WILD-TYPE 202  64
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12               266 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                64 
$`1P LOSS MUTATED`
TCGA-C5-A1MI TCGA-C5-A2LT TCGA-C5-A7CH TCGA-C5-A7UH TCGA-DS-A0VN TCGA-EK-A2PI 
       35.61        73.18       154.32       131.11        95.67        19.27 
TCGA-EK-A3GM TCGA-MY-A913 TCGA-VS-A8EB TCGA-VS-A8Q9 TCGA-VS-A8QH TCGA-VS-A950 
        0.76        17.23        10.03        53.59        39.78        40.14 

$`1P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ 
       30.21        35.01        57.73        53.16        38.99         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
        2.43        20.91        40.93         3.58        44.22        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       210.67       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
      146.86        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       14.73         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       87.75        58.88        36.76        55.63        69.96        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01         0.30 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       27.25        27.22        24.00        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL 
       60.72        26.27         6.64         1.51         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC 
        0.59         0.36         1.45         0.13        40.96         4.31 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.10         0.43        47.77         0.53         0.10         0.49 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92        15.22        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        8.32        15.55         1.22        23.84        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       31.36        36.26        20.98        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       28.31        14.01        35.44        10.55         1.12        17.75 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41        16.57        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       209.59        44.61        20.91        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       12.49         0.30         0.82        13.35        22.52        19.56 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         8.35         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC 
       14.60        11.67        93.99        12.16        69.50        46.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       45.57        32.42        23.97        19.96        65.49        32.15 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       36.13        11.51        59.18        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
        4.73        33.37        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       29.95        27.12        24.30        46.92        45.11         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       14.53        27.25        47.87        47.47        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       15.85        14.53         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 
        5.16        18.25        17.75         4.34        16.24        15.42 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       26.01        29.26        67.59        19.13         0.69         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.76              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           154.32            210.67 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            39.96             22.57 
[1] "0.8 - 154.3 (40.0)" "0.0 - 210.7 (22.6)"
[1] "hr=" "1.5"
D42V2, continuous
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED     4   0   2   0
  1P LOSS WILD-TYPE 131  70  19   8
D42V3, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               4               131
  T2               0                70
  T3               2                19
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3   2
  1P LOSS WILD-TYPE 126  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    2
  1P LOSS WILD-TYPE  126   54
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               3               126
  1               2                54
[1] 2 2
[1] FALSE
D42V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     4   2
  1P LOSS WILD-TYPE 104   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    2
  1P LOSS WILD-TYPE  104    8
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               4               104
  1               2                 8
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1   8
  1P LOSS WILD-TYPE  54 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    8
  1P LOSS WILD-TYPE   54  115
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                1                54
  YES               8               115
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED               0                               11
  1P LOSS WILD-TYPE             6                              231
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1P LOSS MUTATED                                               0
  1P LOSS WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1P LOSS MUTATED                                     1
  1P LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1P LOSS MUTATED                                           0
  1P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1P LOSS MUTATED                                              1
  1P LOSS WILD-TYPE                                           16
D42V7, multiclass
                                               clus
vv                                              1P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           11
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              1P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            231
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, continuous
D42V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     0
  1P LOSS WILD-TYPE                                8    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED                           1
  1P LOSS WILD-TYPE                        27
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           0    11
  1P LOSS WILD-TYPE                                         2   191
D42V10, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               1                27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  11               191
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2   6
  1P LOSS WILD-TYPE  21 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    6
  1P LOSS WILD-TYPE   21  156
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                21
  NOT HISPANIC OR LATINO               6               156
[1] 2 2
[1] FALSE
D42V12, continuous
D42V13, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6   5
  1P LOSS WILD-TYPE 177  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6    5
  1P LOSS WILD-TYPE  177   69
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  TUMOR FREE               6               177
  WITH TUMOR               5                69
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  1P LOSS MUTATED     0   7   4   0   1
  1P LOSS WILD-TYPE  18 122 111   1  23
D42V14, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  G1               0                18
  G2               7               122
  G3               4               111
  G4               0                 1
  GX               1                23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V15, continuous
D42V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  1P LOSS MUTATED                                             0
  1P LOSS WILD-TYPE                                          38
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  1P LOSS MUTATED                                        0
  1P LOSS WILD-TYPE                                      9
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  1P LOSS MUTATED                                                 1
  1P LOSS WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1P LOSS MUTATED                4                   7
  1P LOSS WILD-TYPE             58                 136
D42V17, multiclass
                                                 clus
vv                                                1P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                4
  LIFELONG NON-SMOKER                                           7
                                                 clus
vv                                                1P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    38
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 58
  LIFELONG NON-SMOKER                                           136
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V18, continuous
D42V19, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  0
  1P LOSS WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    0
  1P LOSS WILD-TYPE   23    3
                         clus
vv                        1P LOSS MUTATED 1P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  2                23
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D42V20, continuous
D42V21, continuous
D42V22, continuous
D42V23, continuous
D42V24, continuous
D42V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  1P LOSS MUTATED                                     0
  1P LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  1P LOSS MUTATED                                     0                       2
  1P LOSS WILD-TYPE                                   7                      34
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1P LOSS MUTATED                         0                       0
  1P LOSS WILD-TYPE                       1                       8
D42V26, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                53 
       TCGA-2W-A8YY        TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1BK        TCGA-C5-A1BM        TCGA-C5-A1M5        TCGA-C5-A1M7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME        TCGA-C5-A1MF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1MJ        TCGA-C5-A1MP        TCGA-C5-A2LS        TCGA-C5-A2LV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2M1        TCGA-C5-A3HE        TCGA-C5-A3HL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7CG        TCGA-C5-A7CJ        TCGA-C5-A7UC        TCGA-C5-A7UI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7X8        TCGA-C5-A7XC        TCGA-C5-A8XH        TCGA-C5-A8XI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DG-A2KK        TCGA-DG-A2KL        TCGA-DR-A0ZM        TCGA-DS-A0VK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A3LQ        TCGA-EA-A50E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EK-A2RN        TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-HM-A4S6        TCGA-IR-A3LH        TCGA-IR-A3LI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IR-A3LK        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-UC-A7PD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-VS-A8QA        TCGA-VS-A9UT        TCGA-WL-A834        TCGA-XS-A8TJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ZJ-AAX4 
"1P LOSS WILD-TYPE" 
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  1P LOSS MUTATED                                               0
  1P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  1P LOSS MUTATED                                                1
  1P LOSS WILD-TYPE                                             24
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1P LOSS MUTATED                                                                                   3
  1P LOSS WILD-TYPE                                                                                79
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1P LOSS MUTATED                                                                                              5
  1P LOSS WILD-TYPE                                                                                          116
D42V27, multiclass
                                                                                              clus
vv                                                                                             1P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               5
                                                                                              clus
vv                                                                                             1P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           79
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V28, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  1
  1P LOSS WILD-TYPE 68 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    1
  1P LOSS WILD-TYPE   68   73
         clus
vv        1P LOSS MUTATED 1P LOSS WILD-TYPE
  ABSENT                3                68
  PRESENT               1                73
[1] 2 2
[1] FALSE
D42V29, continuous
D42V30, continuous
D42V31, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3   1
  1P LOSS WILD-TYPE  46 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    1
  1P LOSS WILD-TYPE   46  116
                                          clus
vv                                         1P LOSS MUTATED 1P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   3                46
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               1               116
[1] 2 2
[1] FALSE
D42V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1P LOSS MUTATED              1           2          2
  1P LOSS WILD-TYPE           14          52         83
D42V33, multiclass
              clus
vv             1P LOSS MUTATED 1P LOSS WILD-TYPE
  CURRENT USER               1                14
  FORMER USER                2                52
  NEVER USED                 2                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V34, continuous
D42V35, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    4  0
  1P LOSS WILD-TYPE 88 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    0
  1P LOSS WILD-TYPE   88   18
         clus
vv        1P LOSS MUTATED 1P LOSS WILD-TYPE
  ABSENT                4                88
  PRESENT               0                18
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  1P LOSS MUTATED             0         6     1
  1P LOSS WILD-TYPE           5        94     1
D42V36, multiclass
             clus
vv            1P LOSS MUTATED 1P LOSS WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                 6                94
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V37, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-MA-AA42        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-ZX-AA5X 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D42V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  1P LOSS MUTATED         0        0         0         0        2         3
  1P LOSS WILD-TYPE       5        1         1         1       32        74
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  1P LOSS MUTATED           1        0         2          0          0
  1P LOSS WILD-TYPE        36        4         6          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  1P LOSS MUTATED           1         0          1          3         0
  1P LOSS WILD-TYPE        43         1          2         39         7
                   vv
clus                STAGE IVB
  1P LOSS MUTATED           0
  1P LOSS WILD-TYPE        12
D42V39, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 2                32
  STAGE IB1                3                74
  STAGE IB2                1                36
  STAGE II                 0                 4
  STAGE IIA                2                 6
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                1                43
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               3                39
  STAGE IVA                0                 7
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     6   3
  1Q LOSS WILD-TYPE 205  64
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                9               269 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                64 
$`1Q LOSS MUTATED`
TCGA-C5-A1MI TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CH TCGA-C5-A7UH TCGA-DS-A0VN 
       35.61        73.18        73.45       154.32       131.11        95.67 
TCGA-HM-A3JJ TCGA-MY-A913 TCGA-VS-A8QH 
       21.67        17.23        39.78 

$`1Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ 
       30.21        35.01        57.73        53.16        38.99         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX 
        2.43        20.91        40.93         3.58        44.22        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35       147.35        17.19       155.77        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       13.61         2.73        50.99        45.83         8.35       146.86 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       99.91        23.51        27.52        20.81        20.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        95.11        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76        55.63        69.96        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        31.73        26.01         0.30        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       27.22        24.00        13.48         0.36        12.59        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL 
       26.27         6.64         1.51        19.27         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC 
        0.59         0.36         1.45         0.13        40.96         4.31 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.10         0.43        47.77         0.53         0.10         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.76         0.03        20.35         7.92        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         8.32        15.55         1.22        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
       16.11        31.36        36.26        20.98        26.14         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       17.75        25.41        16.57        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW 
       21.11       209.59        44.61        20.91        11.28         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       12.49         0.30         0.82        13.35        22.52        19.56 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         8.35         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
       14.60        11.67        93.99        12.16        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       46.52        45.57        32.42        23.97        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       32.15        53.59        36.13        11.51        59.18        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       40.87        16.64         4.73        33.37        40.14        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       15.68        56.35        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       43.40        48.39        28.50        29.95        27.12        24.30 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       46.92        45.11         1.71        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
        4.34        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         1.41         0.16         3.91 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            17.23              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           154.32            210.67 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            73.18             22.52 
[1] "17.2 - 154.3 (73.2)" "0.0 - 210.7 (22.5)" 
[1] "hr=" "1.4"
D43V2, continuous
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED     5   0   0   0
  1Q LOSS WILD-TYPE 130  70  21   8
D43V3, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               5               130
  T2               0                70
  T3               0                21
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3   3
  1Q LOSS WILD-TYPE 126  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    3
  1Q LOSS WILD-TYPE  126   53
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               3               126
  1               3                53
[1] 2 2
[1] FALSE
D43V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3   1
  1Q LOSS WILD-TYPE 105   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    1
  1Q LOSS WILD-TYPE  105    9
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               3               105
  1               1                 9
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   5
  1Q LOSS WILD-TYPE  55 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    5
  1Q LOSS WILD-TYPE   55  118
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                0                55
  YES               5               118
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED               0                                8
  1Q LOSS WILD-TYPE             6                              234
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1Q LOSS MUTATED                                               0
  1Q LOSS WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1Q LOSS MUTATED                                     0
  1Q LOSS WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1Q LOSS MUTATED                                           0
  1Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1Q LOSS MUTATED                                              1
  1Q LOSS WILD-TYPE                                           16
D43V7, multiclass
                                               clus
vv                                              1Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            8
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              1Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            234
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, continuous
D43V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     0
  1Q LOSS WILD-TYPE                                8    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED                           3
  1Q LOSS WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0     6
  1Q LOSS WILD-TYPE                                         2   196
D43V10, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               3                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                   6               196
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1   7
  1Q LOSS WILD-TYPE  22 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    7
  1Q LOSS WILD-TYPE   22  155
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                22
  NOT HISPANIC OR LATINO               7               155
[1] 2 2
[1] FALSE
D43V12, continuous
D43V13, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     6   3
  1Q LOSS WILD-TYPE 177  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6    3
  1Q LOSS WILD-TYPE  177   71
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  TUMOR FREE               6               177
  WITH TUMOR               3                71
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  1Q LOSS MUTATED     0   4   5   0   0
  1Q LOSS WILD-TYPE  18 125 110   1  24
D43V14, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  G1               0                18
  G2               4               125
  G3               5               110
  G4               0                 1
  GX               0                24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, continuous
D43V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  1Q LOSS MUTATED                                             0
  1Q LOSS WILD-TYPE                                          38
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  1Q LOSS MUTATED                                        0
  1Q LOSS WILD-TYPE                                      9
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  1Q LOSS MUTATED                                                 1
  1Q LOSS WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1Q LOSS MUTATED                3                   4
  1Q LOSS WILD-TYPE             59                 139
D43V17, multiclass
                                                 clus
vv                                                1Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                3
  LIFELONG NON-SMOKER                                           4
                                                 clus
vv                                                1Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    38
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 59
  LIFELONG NON-SMOKER                                           139
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V18, continuous
D43V19, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  0
  1Q LOSS WILD-TYPE 22  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    0
  1Q LOSS WILD-TYPE   22    3
                         clus
vv                        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  3                22
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D43V20, continuous
D43V21, continuous
D43V22, continuous
D43V23, continuous
D43V24, continuous
D43V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  1Q LOSS MUTATED                                     0
  1Q LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  1Q LOSS MUTATED                                     0                       3
  1Q LOSS WILD-TYPE                                   7                      33
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1Q LOSS MUTATED                         0                       0
  1Q LOSS WILD-TYPE                       1                       8
D43V26, multiclass
                                     clus
vv                                    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           3                33
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  1Q LOSS MUTATED                                               0
  1Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  1Q LOSS MUTATED                                                1
  1Q LOSS WILD-TYPE                                             24
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1Q LOSS MUTATED                                                                                   1
  1Q LOSS WILD-TYPE                                                                                81
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1Q LOSS MUTATED                                                                                              5
  1Q LOSS WILD-TYPE                                                                                          116
D43V27, multiclass
                                                                                              clus
vv                                                                                             1Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          1
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               5
                                                                                              clus
vv                                                                                             1Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           81
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V28, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  2
  1Q LOSS WILD-TYPE 68 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    2
  1Q LOSS WILD-TYPE   68   72
         clus
vv        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ABSENT                3                68
  PRESENT               2                72
[1] 2 2
[1] FALSE
D43V29, continuous
D43V30, continuous
D43V31, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3   2
  1Q LOSS WILD-TYPE  46 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    2
  1Q LOSS WILD-TYPE   46  115
                                          clus
vv                                         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   3                46
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               2               115
[1] 2 2
[1] FALSE
D43V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1Q LOSS MUTATED              1           3          1
  1Q LOSS WILD-TYPE           14          51         84
D43V33, multiclass
              clus
vv             1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CURRENT USER               1                14
  FORMER USER                3                51
  NEVER USED                 1                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V34, continuous
D43V35, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    4  0
  1Q LOSS WILD-TYPE 88 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4    0
  1Q LOSS WILD-TYPE   88   18
         clus
vv        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ABSENT                4                88
  PRESENT               0                18
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  1Q LOSS MUTATED             0         6     1
  1Q LOSS WILD-TYPE           5        94     1
D43V36, multiclass
             clus
vv            1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                 6                94
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V37, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MA-AA42        TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-ZX-AA5X 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D43V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  1Q LOSS MUTATED         0        0         0         0        3         3
  1Q LOSS WILD-TYPE       5        1         1         1       31        74
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  1Q LOSS MUTATED           0        0         1          0          0
  1Q LOSS WILD-TYPE        37        4         7          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  1Q LOSS MUTATED           1         0          0          1         0
  1Q LOSS WILD-TYPE        43         1          3         41         7
                   vv
clus                STAGE IVB
  1Q LOSS MUTATED           0
  1Q LOSS WILD-TYPE        12
D43V39, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 3                31
  STAGE IB1                3                74
  STAGE IB2                0                37
  STAGE II                 0                 4
  STAGE IIA                1                 7
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                1                43
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               1                41
  STAGE IVA                0                 7
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    15   4
  2P LOSS WILD-TYPE 196  63
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               19               259 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                63 
$`2P LOSS MUTATED`
TCGA-BI-A0VS TCGA-C5-A1MH TCGA-C5-A3HE TCGA-C5-A7CG TCGA-DS-A0VN TCGA-EA-A3HR 
       57.04        38.99        18.02       210.67        95.67        30.90 
TCGA-EA-A3QD TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2R8 TCGA-EK-A2RN TCGA-MA-AA43 
       13.05         0.36         1.51         1.45         0.53        11.38 
TCGA-Q1-A5R1 TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A953 TCGA-VS-A9UU 
       15.58        12.16        65.49        11.51        15.68        14.53 
TCGA-XS-A8TJ 
       29.26 

$`2P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       35.01        57.73        53.16        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       20.35       147.35        17.19       155.77       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
        9.34        13.61         2.73        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
      146.86        99.91        23.51        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       14.73         1.12        95.11        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       87.75        58.88        36.76        55.63        69.96        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       37.35        31.53        31.36        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       24.56        31.73        26.01         0.30        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        25.91        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       24.00        13.48        12.59        60.72        26.27         6.64 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 
       19.27         0.39         0.43         0.59         0.36         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ 
       40.96         4.31         0.10         0.43        47.77         0.10 
TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.49         0.76         0.03        20.35         7.92        15.22 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         8.32        15.55         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12        17.75        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        8.28        18.15        21.11       209.59        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        19.56        17.82        19.56         8.35         8.52 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       28.08        34.62        19.96        54.81        35.05        20.84 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       17.23         2.96        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB 
       19.59        14.60        11.67        93.99        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 
       46.52        45.57        32.42        23.97        19.96        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       53.59        36.13        59.18        39.78        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 
       16.64         4.73        33.37        40.14        58.45        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       55.50        50.14        51.32        50.47        43.40        48.39 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       28.50        29.95        27.12        24.30        46.92        45.11 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
        1.71        14.53        27.25        47.87        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       26.07        15.85         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 
        5.16        18.25        17.75         4.34        16.24        15.42 
TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       26.01        67.59        19.13         0.69         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.36              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           210.67            209.59 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            15.58             23.84 
[1] "0.4 - 210.7 (15.6)" "0.0 - 209.6 (23.8)"
[1] "hr=" "1"  
D44V2, continuous
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED     9   4   2   1
  2P LOSS WILD-TYPE 126  66  19   7
D44V3, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               9               126
  T2               4                66
  T3               2                19
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7   5
  2P LOSS WILD-TYPE 122  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7    5
  2P LOSS WILD-TYPE  122   51
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               7               122
  1               5                51
[1] 2 2
[1] FALSE
D44V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     8   0
  2P LOSS WILD-TYPE 100  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      8    0
  2P LOSS WILD-TYPE  100   10
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               8               100
  1               0                10
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3   9
  2P LOSS WILD-TYPE  52 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    9
  2P LOSS WILD-TYPE   52  114
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                3                52
  YES               9               114
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED               0                               18
  2P LOSS WILD-TYPE             6                              224
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2P LOSS MUTATED                                               0
  2P LOSS WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2P LOSS MUTATED                                     0
  2P LOSS WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2P LOSS MUTATED                                           0
  2P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2P LOSS MUTATED                                              1
  2P LOSS WILD-TYPE                                           16
D44V7, multiclass
                                               clus
vv                                              2P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           18
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              2P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            224
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, continuous
D44V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                8    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED                           3
  2P LOSS WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           0    14
  2P LOSS WILD-TYPE                                         2   188
D44V10, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               3                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  14               188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2  10
  2P LOSS WILD-TYPE  21 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   10
  2P LOSS WILD-TYPE   21  152
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                21
  NOT HISPANIC OR LATINO              10               152
[1] 2 2
[1] FALSE
D44V12, continuous
D44V13, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    11   5
  2P LOSS WILD-TYPE 172  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     11    5
  2P LOSS WILD-TYPE  172   69
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  TUMOR FREE              11               172
  WITH TUMOR               5                69
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  2P LOSS MUTATED     2   8   8   0   1
  2P LOSS WILD-TYPE  16 121 107   1  23
D44V14, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  G1               2                16
  G2               8               121
  G3               8               107
  G4               0                 1
  GX               1                23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                41 
       TCGA-2W-A8YY        TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A1BQ        TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A2M2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-C5-A8XH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A907        TCGA-DG-A2KK        TCGA-DS-A3LQ        TCGA-EK-A2RA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EX-A69M        TCGA-FU-A2QG        TCGA-FU-A3TX        TCGA-FU-A3WB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-HM-A4S6        TCGA-IR-A3L7        TCGA-IR-A3LB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-JX-A3Q0        TCGA-MU-A5YI        TCGA-MU-A8JM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-Q1-A73S        TCGA-RA-A741        TCGA-VS-A8QF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-VS-A94Z        TCGA-VS-A9V0        TCGA-VS-A9V4        TCGA-WL-A834 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ZJ-A8QR        TCGA-ZJ-AAX4        TCGA-ZJ-AAXA        TCGA-ZJ-AAXT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ZJ-AB0I 
"2P LOSS WILD-TYPE" 
D44V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2P LOSS MUTATED                                             1
  2P LOSS WILD-TYPE                                          37
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  2P LOSS MUTATED                                        1
  2P LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  2P LOSS MUTATED                                                 1
  2P LOSS WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2P LOSS MUTATED                4                   9
  2P LOSS WILD-TYPE             58                 134
D44V17, multiclass
                                                 clus
vv                                                2P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                4
  LIFELONG NON-SMOKER                                           9
                                                 clus
vv                                                2P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    37
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 58
  LIFELONG NON-SMOKER                                           134
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V18, continuous
D44V19, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    1  0
  2P LOSS WILD-TYPE 24  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    0
  2P LOSS WILD-TYPE   24    3
                         clus
vv                        2P LOSS MUTATED 2P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  1                24
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D44V20, continuous
D44V21, continuous
D44V22, continuous
D44V23, continuous
D44V24, continuous
D44V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  2P LOSS MUTATED                                     0
  2P LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  2P LOSS MUTATED                                     0                       5
  2P LOSS WILD-TYPE                                   7                      31
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2P LOSS MUTATED                         0                       0
  2P LOSS WILD-TYPE                       1                       8
D44V26, multiclass
                                     clus
vv                                    2P LOSS MUTATED 2P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           5                31
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  2P LOSS MUTATED                                               0
  2P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  2P LOSS MUTATED                                                2
  2P LOSS WILD-TYPE                                             23
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2P LOSS MUTATED                                                                                   6
  2P LOSS WILD-TYPE                                                                                76
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2P LOSS MUTATED                                                                                              9
  2P LOSS WILD-TYPE                                                                                          112
D44V27, multiclass
                                                                                              clus
vv                                                                                             2P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               9
                                                                                              clus
vv                                                                                             2P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           76
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V28, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    6  4
  2P LOSS WILD-TYPE 65 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    4
  2P LOSS WILD-TYPE   65   70
         clus
vv        2P LOSS MUTATED 2P LOSS WILD-TYPE
  ABSENT                6                65
  PRESENT               4                70
[1] 2 2
[1] FALSE
D44V29, continuous
D44V30, continuous
D44V31, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     5   9
  2P LOSS WILD-TYPE  44 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    9
  2P LOSS WILD-TYPE   44  108
                                          clus
vv                                         2P LOSS MUTATED 2P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               9               108
[1] 2 2
[1] FALSE
D44V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2P LOSS MUTATED              2           4          5
  2P LOSS WILD-TYPE           13          50         80
D44V33, multiclass
              clus
vv             2P LOSS MUTATED 2P LOSS WILD-TYPE
  CURRENT USER               2                13
  FORMER USER                4                50
  NEVER USED                 5                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V34, continuous
D44V35, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    6  0
  2P LOSS WILD-TYPE 86 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    0
  2P LOSS WILD-TYPE   86   18
         clus
vv        2P LOSS MUTATED 2P LOSS WILD-TYPE
  ABSENT                6                86
  PRESENT               0                18
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  2P LOSS MUTATED             0         8     0
  2P LOSS WILD-TYPE           5        92     2
D44V36, multiclass
             clus
vv            2P LOSS MUTATED 2P LOSS WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                 8                92
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V37, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A1MP 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D44V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  2P LOSS MUTATED         0        0         0         0        3         3
  2P LOSS WILD-TYPE       5        1         1         1       31        74
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  2P LOSS MUTATED           3        1         0          0          0
  2P LOSS WILD-TYPE        34        3         8          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  2P LOSS MUTATED           2         0          0          4         2
  2P LOSS WILD-TYPE        42         1          3         38         5
                   vv
clus                STAGE IVB
  2P LOSS MUTATED           0
  2P LOSS WILD-TYPE        12
D44V39, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 3                31
  STAGE IB1                3                74
  STAGE IB2                3                34
  STAGE II                 1                 3
  STAGE IIA                0                 8
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                2                42
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               4                38
  STAGE IVA                2                 5
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    26   9
  2Q LOSS WILD-TYPE 185  58
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               35               243 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                9                58 
$`2Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A3HE TCGA-C5-A7CG 
       57.04        36.56        30.21        38.99        18.02       210.67 
TCGA-C5-A8YR TCGA-DG-A2KL TCGA-DS-A0VN TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A411 
       27.52        44.94        95.67        30.90        13.05        24.56 
TCGA-EA-A44S TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2R8 TCGA-EK-A2RN TCGA-EX-A69L 
        0.30         0.36         1.51         1.45         0.53        19.79 
TCGA-HM-A3JJ TCGA-JX-A5QV TCGA-LP-A7HU TCGA-MA-AA43 TCGA-MY-A5BF TCGA-Q1-A5R1 
       21.67        20.91        13.35        11.38        20.84        15.58 
TCGA-Q1-A5R2 TCGA-UC-A7PG TCGA-VS-A8EL TCGA-VS-A8QC TCGA-VS-A953 TCGA-VS-A9UI 
       16.41        12.16        65.49        11.51        15.68        45.11 
TCGA-VS-A9UM TCGA-VS-A9UU TCGA-VS-A9V5 TCGA-XS-A8TJ TCGA-ZJ-AAX4 
       27.25        14.53        16.24        29.26         0.69 

$`2Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       18.74       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME 
       19.86        67.46        31.40        46.32        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       53.16        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43        33.24        52.01        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19       155.77       131.11        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       23.51        20.81        20.91        14.73         1.12        95.11 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       82.06        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       69.96        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
       39.55        40.87        37.35        31.53        31.36        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E 
       36.89        26.40        31.73        26.01        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        25.91        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       24.00        13.48        12.59        60.72        26.27         6.64 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 
       19.27         0.39         0.43         0.59         0.36         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GJ 
       40.96         4.31         0.10         0.43        47.77         0.10 
TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.49         0.76         0.03        20.35         7.92        15.22 
TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         8.32        15.55         1.22        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
       16.11        31.36        36.26        20.98        26.14         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       17.75        25.41        16.57        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        44.61        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.30         0.82        22.52        19.56        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.35         8.52        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       35.05        17.23         2.96        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB 
       19.59        14.60        11.67        93.99        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 
       46.52        45.57        32.42        23.97        19.96        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       53.59        36.13        59.18        39.78        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 
       16.64         4.73        33.37        40.14        58.45        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 
       55.50        50.14        51.32        50.47        43.40        48.39 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ 
       28.50        29.95        27.12        24.30        46.92         1.71 
TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       14.53        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       17.75         4.34        15.42        26.01        67.59        19.13 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.30              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           210.67            209.59 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            19.79             23.97 
[1] "0.3 - 210.7 (19.8)" "0.0 - 209.6 (24.0)"
[1] "hr=" "1.4"
D45V2, continuous
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED    15  11   3   1
  2Q LOSS WILD-TYPE 120  59  18   7
D45V3, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1              15               120
  T2              11                59
  T3               3                18
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    16   7
  2Q LOSS WILD-TYPE 113  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     16    7
  2Q LOSS WILD-TYPE  113   49
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              16               113
  1               7                49
[1] 2 2
[1] FALSE
D45V5, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   16  0
  2Q LOSS WILD-TYPE 92 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     16    0
  2Q LOSS WILD-TYPE   92   10
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              16                92
  1               0                10
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7  13
  2Q LOSS WILD-TYPE  48 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7   13
  2Q LOSS WILD-TYPE   48  110
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                7                48
  YES              13               110
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED               0                               32
  2Q LOSS WILD-TYPE             6                              210
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2Q LOSS MUTATED                                               0
  2Q LOSS WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2Q LOSS MUTATED                                     1
  2Q LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2Q LOSS MUTATED                                           0
  2Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2Q LOSS MUTATED                                              2
  2Q LOSS WILD-TYPE                                           15
D45V7, multiclass
                                               clus
vv                                              2Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           32
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              2Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            210
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, continuous
D45V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     2
  2Q LOSS WILD-TYPE                                8    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED                           5
  2Q LOSS WILD-TYPE                        23
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           0    25
  2Q LOSS WILD-TYPE                                         2   177
D45V10, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               5                23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  25               177
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  22
  2Q LOSS WILD-TYPE  21 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   22
  2Q LOSS WILD-TYPE   21  140
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                21
  NOT HISPANIC OR LATINO              22               140
[1] 2 2
[1] FALSE
D45V12, continuous
D45V13, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    23   7
  2Q LOSS WILD-TYPE 160  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     23    7
  2Q LOSS WILD-TYPE  160   67
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  TUMOR FREE              23               160
  WITH TUMOR               7                67
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  2Q LOSS MUTATED     4  14  15   0   2
  2Q LOSS WILD-TYPE  14 115 100   1  22
D45V14, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  G1               4                14
  G2              14               115
  G3              15               100
  G4               0                 1
  GX               2                22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, continuous
D45V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2Q LOSS MUTATED                                             2
  2Q LOSS WILD-TYPE                                          36
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  2Q LOSS MUTATED                                        1
  2Q LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  2Q LOSS MUTATED                                                 1
  2Q LOSS WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2Q LOSS MUTATED                6                  21
  2Q LOSS WILD-TYPE             56                 122
D45V17, multiclass
                                                 clus
vv                                                2Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                6
  LIFELONG NON-SMOKER                                          21
                                                 clus
vv                                                2Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 56
  LIFELONG NON-SMOKER                                           122
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V18, continuous
D45V19, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    4  0
  2Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4    0
  2Q LOSS WILD-TYPE   21    3
                         clus
vv                        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  4                21
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D45V20, continuous
D45V21, continuous
D45V22, continuous
D45V23, continuous
D45V24, continuous
D45V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  2Q LOSS MUTATED                                     0
  2Q LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  2Q LOSS MUTATED                                     0                       6
  2Q LOSS WILD-TYPE                                   7                      30
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2Q LOSS MUTATED                         0                       2
  2Q LOSS WILD-TYPE                       1                       6
D45V26, multiclass
                                     clus
vv                                    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           6                30
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  2Q LOSS MUTATED                                               1
  2Q LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  2Q LOSS MUTATED                                                3
  2Q LOSS WILD-TYPE                                             22
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2Q LOSS MUTATED                                                                                  12
  2Q LOSS WILD-TYPE                                                                                70
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2Q LOSS MUTATED                                                                                             15
  2Q LOSS WILD-TYPE                                                                                          106
D45V27, multiclass
                                                                                              clus
vv                                                                                             2Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              15
                                                                                              clus
vv                                                                                             2Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V28, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   11  8
  2Q LOSS WILD-TYPE 60 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11    8
  2Q LOSS WILD-TYPE   60   66
         clus
vv        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ABSENT               11                60
  PRESENT               8                66
[1] 2 2
[1] FALSE
D45V29, continuous
D45V30, continuous
D45V31, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7  16
  2Q LOSS WILD-TYPE  42 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7   16
  2Q LOSS WILD-TYPE   42  101
                                          clus
vv                                         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   7                42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              16               101
[1] 2 2
[1] FALSE
D45V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2Q LOSS MUTATED              2           8         14
  2Q LOSS WILD-TYPE           13          46         71
D45V33, multiclass
              clus
vv             2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CURRENT USER               2                13
  FORMER USER                8                46
  NEVER USED                14                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V34, continuous
D45V35, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   12  0
  2Q LOSS WILD-TYPE 80 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     12    0
  2Q LOSS WILD-TYPE   80   18
         clus
vv        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ABSENT               12                80
  PRESENT               0                18
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  2Q LOSS MUTATED             1        12     0
  2Q LOSS WILD-TYPE           4        88     2
D45V36, multiclass
             clus
vv            2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                12                88
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V37, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A1MP 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D45V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  2Q LOSS MUTATED         0        0         0         0        4         8
  2Q LOSS WILD-TYPE       5        1         1         1       30        69
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  2Q LOSS MUTATED           3        3         1          0          1
  2Q LOSS WILD-TYPE        34        1         7          5          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  2Q LOSS MUTATED           4         0          0          6         2
  2Q LOSS WILD-TYPE        40         1          3         36         5
                   vv
clus                STAGE IVB
  2Q LOSS MUTATED           1
  2Q LOSS WILD-TYPE        11
D45V39, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 4                30
  STAGE IB1                8                69
  STAGE IB2                3                34
  STAGE II                 3                 1
  STAGE IIA                1                 7
  STAGE IIA1               0                 5
  STAGE IIA2               1                 6
  STAGE IIB                4                40
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               6                36
  STAGE IVA                2                 5
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    53  22
  3P LOSS WILD-TYPE 158  45
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               75               203 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22                45 
$`3P LOSS MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BL 
       49.48        23.67        11.44        18.74        36.56       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LX 
       82.85         5.46        31.40        35.61        40.93        83.05 
TCGA-C5-A7CH TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 
      154.32       147.35       155.77        94.95        13.61         2.73 
TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KM TCGA-DR-A0ZL 
       45.83       146.86        23.51        20.91        63.98        87.75 
TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-EA-A3HS TCGA-EA-A3QD 
       36.76        69.96        95.67        16.83        31.53        13.05 
TCGA-EA-A3QE TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A97N 
       25.02        24.56         0.30        27.25        24.00         0.36 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2RC TCGA-EX-A1H5 TCGA-FU-A23L 
        6.64         0.43         0.36         4.31        20.35        23.84 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A5XV TCGA-IR-A3L7 TCGA-JW-A5VI 
       31.36        20.98        28.31        10.55       147.39        24.56 
TCGA-JW-A5VJ TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-MA-AA42 TCGA-MU-A5YI TCGA-MY-A913 
       21.44        18.15        21.11         8.52        34.62        17.23 
TCGA-Q1-A5R2 TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF TCGA-VS-A8EC 
       16.41         9.34        22.62        14.60        93.99        46.52 
TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       32.15        11.51        39.78         4.73        33.37        40.14 
TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-XS-A8TJ 
       50.47        28.50        14.53        27.25        47.47        29.26 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU 
       19.13         0.69         0.16 

$`3P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BK 
       17.52        17.82        57.04        68.84       144.16       177.04 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       19.86        67.46        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP 
       53.16        38.99         0.46         2.43        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.18        73.45        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH 
      101.82       134.33        15.48        20.35        17.19       131.11 
TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
        9.34        50.99         8.35        99.91        27.52        20.81 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM 
       14.73         1.12        95.11        82.06        44.94        58.88 
TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       55.63        22.98        16.18        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3Y4 TCGA-EA-A410 
       40.87        37.35        30.90        31.36        36.89        26.40 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       31.73        26.01        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       25.91        27.29        27.22        13.48        12.59        60.72 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R8 
       26.27         1.51        19.27         0.39         0.59         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
        0.13        40.96         0.10         0.43        47.77         0.53 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.49         0.76         0.03         7.92        15.22 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG 
       14.70        19.79         8.32        15.55         1.22        19.04 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A40J 
       16.11        36.26        26.14         1.48        16.14        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44         1.12        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       20.78        14.93         9.44       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3Q0 
        3.29        20.48        15.58        28.37         8.28       209.59 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
       44.61        20.91        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.82        13.35        22.52        19.56        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        8.35        11.38        28.08        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       20.84         2.96        15.58        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD 
       17.56        14.07        15.88        18.64        19.59        11.67 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       12.16        69.50        10.03        45.57        32.42        23.97 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QM 
       19.96        65.49        53.59        36.13        59.18        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       40.87        16.64        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UC 
       50.14        51.32        43.40        48.39        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ 
       24.30        46.92        45.11         1.71        47.87        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       26.07        15.85        14.53         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.84         5.16        18.25        17.75         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       15.42        26.01        67.59         1.41         3.91 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.16              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           173.29            210.67 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            24.56             20.84 
[1] "0.2 - 173.3 (24.6)" "0.0 - 210.7 (20.8)"
[1] "hr=" "1.1"
D46V2, continuous
                   vv
clus                 T1  T2  T3  T4
  3P LOSS MUTATED    34  17   7   0
  3P LOSS WILD-TYPE 101  53  14   8
D46V3, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              34               101
  T2              17                53
  T3               7                14
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    26  22
  3P LOSS WILD-TYPE 103  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     26   22
  3P LOSS WILD-TYPE  103   34
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              26               103
  1              22                34
[1] 2 2
[1] FALSE
D46V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   31  1
  3P LOSS WILD-TYPE 77  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     31    1
  3P LOSS WILD-TYPE   77    9
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              31                77
  1               1                 9
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   11 32
  3P LOSS WILD-TYPE 44 91
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     11   32
  3P LOSS WILD-TYPE   44   91
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               11                44
  YES              32                91
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED               1                               77
  3P LOSS WILD-TYPE             5                              165
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3P LOSS MUTATED                                               1
  3P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3P LOSS MUTATED                                     0
  3P LOSS WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3P LOSS MUTATED                                           0
  3P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3P LOSS MUTATED                                              3
  3P LOSS WILD-TYPE                                           14
D46V7, multiclass
                                               clus
vv                                              3P LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           77
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                3
                                               clus
vv                                              3P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            165
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, continuous
D46V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  2     3
  3P LOSS WILD-TYPE                                6    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED                           9
  3P LOSS WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           1    60
  3P LOSS WILD-TYPE                                         1   142
D46V10, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 6
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               9                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 1
  WHITE                                                  60               142
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     6  50
  3P LOSS WILD-TYPE  17 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6   50
  3P LOSS WILD-TYPE   17  112
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                17
  NOT HISPANIC OR LATINO              50               112
[1] 2 2
[1] FALSE
D46V12, continuous
D46V13, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    47  21
  3P LOSS WILD-TYPE 136  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     47   21
  3P LOSS WILD-TYPE  136   53
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  TUMOR FREE              47               136
  WITH TUMOR              21                53
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  3P LOSS MUTATED    3 37 33  0  4
  3P LOSS WILD-TYPE 15 92 82  1 20
D46V14, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  G1               3                15
  G2              37                92
  G3              33                82
  G4               0                 1
  GX               4                20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, continuous
D46V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3P LOSS MUTATED                                            11
  3P LOSS WILD-TYPE                                          27
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  3P LOSS MUTATED                                        2
  3P LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  3P LOSS MUTATED                                                 2
  3P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3P LOSS MUTATED               28                  29
  3P LOSS WILD-TYPE             34                 114
D46V17, multiclass
                                                 clus
vv                                                3P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               2
  CURRENT SMOKER                                               28
  LIFELONG NON-SMOKER                                          29
                                                 clus
vv                                                3P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    27
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 34
  LIFELONG NON-SMOKER                                           114
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V18, continuous
D46V19, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   10  1
  3P LOSS WILD-TYPE 15  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10    1
  3P LOSS WILD-TYPE   15    2
                         clus
vv                        3P LOSS MUTATED 3P LOSS WILD-TYPE
  COMPLETED AS PLANNED                 10                15
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D46V20, continuous
D46V21, continuous
D46V22, continuous
D46V23, continuous
D46V24, continuous
D46V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  3P LOSS MUTATED                                     0
  3P LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  3P LOSS MUTATED                                     3                       6
  3P LOSS WILD-TYPE                                   4                      30
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3P LOSS MUTATED                         0                       4
  3P LOSS WILD-TYPE                       1                       4
D46V26, multiclass
                                     clus
vv                                    3P LOSS MUTATED 3P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               3                 4
  OTHER LOCATION, SPECIFY                           6                30
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           4                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  3P LOSS MUTATED                                               0
  3P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  3P LOSS MUTATED                                                8
  3P LOSS WILD-TYPE                                             17
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3P LOSS MUTATED                                                                                  20
  3P LOSS WILD-TYPE                                                                                62
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3P LOSS MUTATED                                                                                             33
  3P LOSS WILD-TYPE                                                                                           88
D46V27, multiclass
                                                                                              clus
vv                                                                                             3P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              33
                                                                                              clus
vv                                                                                             3P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           62
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V28, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   11 29
  3P LOSS WILD-TYPE 60 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     11   29
  3P LOSS WILD-TYPE   60   45
         clus
vv        3P LOSS MUTATED 3P LOSS WILD-TYPE
  ABSENT               11                60
  PRESENT              29                45
[1] 2 2
[1] FALSE
D46V29, continuous
D46V30, continuous
D46V31, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   17 35
  3P LOSS WILD-TYPE 32 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     17   35
  3P LOSS WILD-TYPE   32   82
                                          clus
vv                                         3P LOSS MUTATED 3P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  17                32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              35                82
[1] 2 2
[1] FALSE
D46V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3P LOSS MUTATED              2          19         19
  3P LOSS WILD-TYPE           13          35         66
D46V33, multiclass
              clus
vv             3P LOSS MUTATED 3P LOSS WILD-TYPE
  CURRENT USER               2                13
  FORMER USER               19                35
  NEVER USED                19                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V34, continuous
D46V35, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   22  6
  3P LOSS WILD-TYPE 70 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     22    6
  3P LOSS WILD-TYPE   70   12
         clus
vv        3P LOSS MUTATED 3P LOSS WILD-TYPE
  ABSENT               22                70
  PRESENT               6                12
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  3P LOSS MUTATED             1        27     1
  3P LOSS WILD-TYPE           4        73     1
D46V36, multiclass
             clus
vv            3P LOSS MUTATED 3P LOSS WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                27                73
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V37, continuous
D46V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  3P LOSS MUTATED         2        0         1         0       13        22
  3P LOSS WILD-TYPE       3        1         0         1       21        55
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  3P LOSS MUTATED           7        1         3          1          0
  3P LOSS WILD-TYPE        30        3         5          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  3P LOSS MUTATED          12         0          2         12         1
  3P LOSS WILD-TYPE        32         1          1         30         6
                   vv
clus                STAGE IVB
  3P LOSS MUTATED           3
  3P LOSS WILD-TYPE         9
D46V39, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 0                 1
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                13                21
  STAGE IB1               22                55
  STAGE IB2                7                30
  STAGE II                 1                 3
  STAGE IIA                3                 5
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB               12                32
  STAGE III                0                 1
  STAGE IIIA               2                 1
  STAGE IIIB              12                30
  STAGE IVA                1                 6
  STAGE IVB                3                 9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     7   3
  3Q LOSS WILD-TYPE 204  64
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               268 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                64 
$`3Q LOSS MUTATED`
TCGA-C5-A7CH TCGA-C5-A7X5 TCGA-EA-A411 TCGA-EK-A2PL TCGA-JX-A3PZ TCGA-MA-AA42 
      154.32        13.61        24.56         0.43        21.11         8.52 
TCGA-MU-A5YI TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-VS-A8QH 
       34.62         9.34        22.62        39.78 

$`3Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       30.21        35.01        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC 
      155.77       131.11        94.95         9.34         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       45.83         8.35       146.86        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       20.81        20.91        14.73         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       69.96        95.67        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 
       31.36        13.05        25.02        36.89        26.40        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
        0.36        12.59        60.72        26.27         6.64         1.51 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       19.27         0.39         0.59         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
       40.96         4.31         0.10         0.43        47.77         0.53 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.49         0.76         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       15.22        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
       26.14         1.48        16.14        28.31        14.01        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       10.55         1.12        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       28.37         8.28        18.15       209.59        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       11.28         0.89        12.49         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 
       22.52        19.56        17.82        19.56         8.35        11.38 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       28.08        19.96        54.81        35.05        20.84        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
       17.56        14.07        15.88        18.64        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        69.50        10.03        46.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       45.57        32.42        23.97        19.96        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       53.59        36.13        11.51        59.18        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       16.64         4.73        33.37        40.14        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       56.35        55.50        50.14        51.32        50.47        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       48.39        28.50        29.95        27.12        24.30        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       45.11         1.71        14.53        27.25        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       41.52        26.07        15.85        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       67.20        18.84         5.16        18.25        17.75         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.43              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           154.32            210.67 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           21.865            23.590 
[1] "0.4 - 154.3 (21.9)" "0.0 - 210.7 (23.6)"
[1] "hr=" "1.3"
D47V2, continuous
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED     6   1   1   0
  3Q LOSS WILD-TYPE 129  69  20   8
D47V3, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               6               129
  T2               1                69
  T3               1                20
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     4   3
  3Q LOSS WILD-TYPE 125  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    3
  3Q LOSS WILD-TYPE  125   53
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               4               125
  1               3                53
[1] 2 2
[1] FALSE
D47V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5   0
  3Q LOSS WILD-TYPE 103  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    0
  3Q LOSS WILD-TYPE  103   10
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               5               103
  1               0                10
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2   6
  3Q LOSS WILD-TYPE  53 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    6
  3Q LOSS WILD-TYPE   53  117
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                2                53
  YES               6               117
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED               1                               12
  3Q LOSS WILD-TYPE             5                              230
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3Q LOSS MUTATED                                               0
  3Q LOSS WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3Q LOSS MUTATED                                     0
  3Q LOSS WILD-TYPE                                  21
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3Q LOSS MUTATED                                           0
  3Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3Q LOSS MUTATED                                              1
  3Q LOSS WILD-TYPE                                           16
D47V7, multiclass
                                               clus
vv                                              3Q LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           12
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              3Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            230
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, continuous
D47V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                8    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED                           2
  3Q LOSS WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           0    11
  3Q LOSS WILD-TYPE                                         2   191
D47V10, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               2                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  11               191
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1   9
  3Q LOSS WILD-TYPE  22 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    9
  3Q LOSS WILD-TYPE   22  153
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                22
  NOT HISPANIC OR LATINO               9               153
[1] 2 2
[1] FALSE
D47V12, continuous
D47V13, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     4   6
  3Q LOSS WILD-TYPE 179  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    6
  3Q LOSS WILD-TYPE  179   68
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  TUMOR FREE               4               179
  WITH TUMOR               6                68
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  3Q LOSS MUTATED     0   7   3   0   1
  3Q LOSS WILD-TYPE  18 122 112   1  23
D47V14, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  G1               0                18
  G2               7               122
  G3               3               112
  G4               0                 1
  GX               1                23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V15, continuous
D47V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3Q LOSS MUTATED                                             2
  3Q LOSS WILD-TYPE                                          36
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  3Q LOSS MUTATED                                        1
  3Q LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  3Q LOSS MUTATED                                                 0
  3Q LOSS WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3Q LOSS MUTATED                2                   5
  3Q LOSS WILD-TYPE             60                 138
D47V17, multiclass
                                                 clus
vv                                                3Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                2
  LIFELONG NON-SMOKER                                           5
                                                 clus
vv                                                3Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 60
  LIFELONG NON-SMOKER                                           138
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V18, continuous
D47V19, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    0  0
  3Q LOSS WILD-TYPE 25  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    0
  3Q LOSS WILD-TYPE   25    3
D47V20, continuous
D47V21, continuous
D47V22, continuous
D47V23, continuous
D47V24, continuous
D47V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  3Q LOSS MUTATED                                     0
  3Q LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  3Q LOSS MUTATED                                     0                       0
  3Q LOSS WILD-TYPE                                   7                      36
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3Q LOSS MUTATED                         0                       0
  3Q LOSS WILD-TYPE                       1                       8
D47V26, multiclass
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  3Q LOSS MUTATED                                               0
  3Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  3Q LOSS MUTATED                                                0
  3Q LOSS WILD-TYPE                                             25
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3Q LOSS MUTATED                                                                                   4
  3Q LOSS WILD-TYPE                                                                                78
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3Q LOSS MUTATED                                                                                              3
  3Q LOSS WILD-TYPE                                                                                          118
D47V27, multiclass
                                                                                              clus
vv                                                                                             3Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               3
                                                                                              clus
vv                                                                                             3Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              25
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           78
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V28, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  4
  3Q LOSS WILD-TYPE 70 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    4
  3Q LOSS WILD-TYPE   70   70
         clus
vv        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ABSENT                1                70
  PRESENT               4                70
[1] 2 2
[1] FALSE
D47V29, continuous
D47V30, continuous
D47V31, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     4   9
  3Q LOSS WILD-TYPE  45 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    9
  3Q LOSS WILD-TYPE   45  108
                                          clus
vv                                         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   4                45
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               9               108
[1] 2 2
[1] FALSE
D47V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3Q LOSS MUTATED              0           2          1
  3Q LOSS WILD-TYPE           15          52         84
D47V33, multiclass
              clus
vv             3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CURRENT USER               0                15
  FORMER USER                2                52
  NEVER USED                 1                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V34, continuous
D47V35, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  1
  3Q LOSS WILD-TYPE 90 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    1
  3Q LOSS WILD-TYPE   90   17
         clus
vv        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ABSENT                2                90
  PRESENT               1                17
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  3Q LOSS MUTATED             1         3     1
  3Q LOSS WILD-TYPE           4        97     1
D47V36, multiclass
             clus
vv            3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                 3                97
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V37, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D47V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  3Q LOSS MUTATED         1        0         1         0        1         3
  3Q LOSS WILD-TYPE       4        1         0         1       33        74
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  3Q LOSS MUTATED           2        0         0          0          0
  3Q LOSS WILD-TYPE        35        4         8          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  3Q LOSS MUTATED           2         0          0          2         0
  3Q LOSS WILD-TYPE        42         1          3         40         7
                   vv
clus                STAGE IVB
  3Q LOSS MUTATED           1
  3Q LOSS WILD-TYPE        11
D47V39, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                 1                33
  STAGE IB1                3                74
  STAGE IB2                2                35
  STAGE II                 0                 4
  STAGE IIA                0                 8
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                2                42
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               2                40
  STAGE IVA                0                 7
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    90  33
  4P LOSS WILD-TYPE 121  34
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              123               155 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               33                34 
$`4P LOSS MUTATED`
TCGA-BI-A0VR TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        11.44        68.84        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MI 
      173.29         5.46        31.40        35.01        53.16        35.61 
TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ 
       20.91         3.58        73.18        73.45        83.05       100.14 
TCGA-C5-A3HE TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
       18.02       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK 
      131.11        94.95         9.34         2.73        45.83        99.91 
TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VK 
       23.51        20.91        95.11        63.98        87.75        36.76 
TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
       55.63        95.67        16.83        40.87        30.90        31.53 
TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A78R 
       36.89        24.56        31.73        26.01         0.30        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PM 
        0.36        12.59        26.27         1.51         0.39         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RN 
        0.36         1.45        40.96         0.10         0.43         0.53 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI 
        0.49        20.35        15.22        23.84        31.36        20.98 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-JW-A5VK 
       10.55        17.75        16.57        21.67        78.71        20.48 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-MA-AA3W 
       20.91        11.28         0.89        12.49         0.30        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA43 TCGA-MU-A8JM TCGA-MY-A5BF TCGA-MY-A913 
       19.56        19.56        11.38        19.96        20.84        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A73S TCGA-UC-A7PD 
        2.96        16.41        15.95         9.04        22.62        11.67 
TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       12.16        10.03        46.52        45.57        32.42        23.97 
TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       19.96        32.15        11.51        59.18        31.27        40.87 
TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       40.14        15.68        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       43.40        24.30        45.11        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-WL-A834 
       47.47        15.85         3.42        18.25         4.34        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAXA 
       29.26        19.13         1.41 

$`4P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BM 
       17.52        17.82        57.04        23.67        18.74        82.85 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MH 
       19.86        67.46        46.32        30.21        57.73        38.99 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2M1 
        0.46         2.43        40.93        44.22        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       33.24        52.01        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7UE TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ 
      101.82       155.77        13.61        50.99         8.35       146.86 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL 
       27.52        20.81        14.73         1.12        82.06        44.94 
TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       58.88        69.96        22.98        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 
       39.55        37.35        31.36        13.05        25.02        26.40 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PI 
       27.25        27.22        24.00        60.72         6.64        19.27 
TCGA-EK-A2PL TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GM 
        0.43         0.13         4.31        47.77         0.10         0.76 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        0.03         7.92        14.70        19.79         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        1.22        19.04        16.11        36.26        26.14         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA 
       16.14        28.31        14.01        35.44         1.12        25.41 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      129.37        96.95        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        21.44        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A5U3 TCGA-LP-A7HU 
       18.15        21.11       209.59        44.61         0.82        13.35 
TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD 
       17.82         8.35         8.52        28.08        34.62        54.81 
TCGA-MY-A5BE TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       35.05        15.58        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI 
        9.34        18.64        19.59        14.60        93.99        69.50 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y 
       65.49        53.59        36.13        39.78        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       33.37        58.45        56.35        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU 
       27.12        46.92         1.71        41.52        26.07        14.53 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 
       18.25        67.20        18.84         5.16        17.75        16.24 
TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       15.42        67.59         0.69         0.16         3.91 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.10              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           177.04            210.67 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            22.52             24.00 
[1] "0.1 - 177.0 (22.5)" "0.0 - 210.7 (24.0)"
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED   55 28 14  4
  4P LOSS WILD-TYPE 80 42  7  4
D48V3, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              55                80
  T2              28                42
  T3              14                 7
  T4               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   45 32
  4P LOSS WILD-TYPE 84 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     45   32
  4P LOSS WILD-TYPE   84   24
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              45                84
  1              32                24
[1] 2 2
[1] FALSE
D48V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   43  5
  4P LOSS WILD-TYPE 65  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     43    5
  4P LOSS WILD-TYPE   65    5
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              43                65
  1               5                 5
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   17 62
  4P LOSS WILD-TYPE 38 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     17   62
  4P LOSS WILD-TYPE   38   61
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               17                38
  YES              62                61
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED               2                              119
  4P LOSS WILD-TYPE             4                              123
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4P LOSS MUTATED                                               3
  4P LOSS WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4P LOSS MUTATED                                     2
  4P LOSS WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4P LOSS MUTATED                                           0
  4P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4P LOSS MUTATED                                              5
  4P LOSS WILD-TYPE                                           12
D48V7, multiclass
                                               clus
vv                                              4P LOSS MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                          119
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                5
                                               clus
vv                                              4P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, continuous
D48V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  2     8
  4P LOSS WILD-TYPE                                6    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED                          17
  4P LOSS WILD-TYPE                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           1    88
  4P LOSS WILD-TYPE                                         1   114
D48V10, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 6
  ASIAN                                                   8                11
  BLACK OR AFRICAN AMERICAN                              17                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 1
  WHITE                                                  88               114
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    7 73
  4P LOSS WILD-TYPE 16 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      7   73
  4P LOSS WILD-TYPE   16   89
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                16
  NOT HISPANIC OR LATINO              73                89
[1] 2 2
[1] FALSE
D48V12, continuous
D48V13, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    81  33
  4P LOSS WILD-TYPE 102  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     81   33
  4P LOSS WILD-TYPE  102   41
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  TUMOR FREE              81               102
  WITH TUMOR              33                41
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  4P LOSS MUTATED    4 54 57  1 11
  4P LOSS WILD-TYPE 14 75 58  0 13
D48V14, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  G1               4                14
  G2              54                75
  G3              57                58
  G4               1                 0
  GX              11                13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, continuous
D48V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4P LOSS MUTATED                                            16
  4P LOSS WILD-TYPE                                          22
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  4P LOSS MUTATED                                        4
  4P LOSS WILD-TYPE                                      5
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  4P LOSS MUTATED                                                 3
  4P LOSS WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4P LOSS MUTATED               29                  56
  4P LOSS WILD-TYPE             33                  87
D48V17, multiclass
                                                 clus
vv                                                4P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               3
  CURRENT SMOKER                                               29
  LIFELONG NON-SMOKER                                          56
                                                 clus
vv                                                4P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 33
  LIFELONG NON-SMOKER                                            87
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V18, continuous
D48V19, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   14  1
  4P LOSS WILD-TYPE 11  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     14    1
  4P LOSS WILD-TYPE   11    2
                         clus
vv                        4P LOSS MUTATED 4P LOSS WILD-TYPE
  COMPLETED AS PLANNED                 14                11
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D48V20, continuous
D48V21, continuous
D48V22, continuous
D48V23, continuous
D48V24, continuous
D48V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  4P LOSS MUTATED                                     0
  4P LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  4P LOSS MUTATED                                     4                      18
  4P LOSS WILD-TYPE                                   3                      18
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4P LOSS MUTATED                         0                       3
  4P LOSS WILD-TYPE                       1                       5
D48V26, multiclass
                                     clus
vv                                    4P LOSS MUTATED 4P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               4                 3
  OTHER LOCATION, SPECIFY                          18                18
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           3                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  4P LOSS MUTATED                                               0
  4P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  4P LOSS MUTATED                                               14
  4P LOSS WILD-TYPE                                             11
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4P LOSS MUTATED                                                                                  37
  4P LOSS WILD-TYPE                                                                                45
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4P LOSS MUTATED                                                                                             52
  4P LOSS WILD-TYPE                                                                                           69
D48V27, multiclass
                                                                                              clus
vv                                                                                             4P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                            14
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         37
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              52
                                                                                              clus
vv                                                                                             4P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              11
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V28, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   25 34
  4P LOSS WILD-TYPE 46 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     25   34
  4P LOSS WILD-TYPE   46   40
         clus
vv        4P LOSS MUTATED 4P LOSS WILD-TYPE
  ABSENT               25                46
  PRESENT              34                40
[1] 2 2
[1] FALSE
D48V29, continuous
D48V30, continuous
D48V31, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   26 51
  4P LOSS WILD-TYPE 23 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     26   51
  4P LOSS WILD-TYPE   23   66
                                          clus
vv                                         4P LOSS MUTATED 4P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  26                23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              51                66
[1] 2 2
[1] FALSE
D48V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4P LOSS MUTATED              5          23         39
  4P LOSS WILD-TYPE           10          31         46
D48V33, multiclass
              clus
vv             4P LOSS MUTATED 4P LOSS WILD-TYPE
  CURRENT USER               5                10
  FORMER USER               23                31
  NEVER USED                39                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V34, continuous
D48V35, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   33  7
  4P LOSS WILD-TYPE 59 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     33    7
  4P LOSS WILD-TYPE   59   11
         clus
vv        4P LOSS MUTATED 4P LOSS WILD-TYPE
  ABSENT               33                59
  PRESENT               7                11
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  4P LOSS MUTATED             0        50     1
  4P LOSS WILD-TYPE           5        50     1
D48V36, multiclass
             clus
vv            4P LOSS MUTATED 4P LOSS WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                50                50
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V37, continuous
D48V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  4P LOSS MUTATED         2        1         0         1       17        29
  4P LOSS WILD-TYPE       3        0         1         0       17        48
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  4P LOSS MUTATED          17        1         2          4          2
  4P LOSS WILD-TYPE        20        3         6          1          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  4P LOSS MUTATED          19         0          2         21         5
  4P LOSS WILD-TYPE        25         1          1         21         2
                   vv
clus                STAGE IVB
  4P LOSS MUTATED           3
  4P LOSS WILD-TYPE         9
D48V39, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 1                 0
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                17                17
  STAGE IB1               29                48
  STAGE IB2               17                20
  STAGE II                 1                 3
  STAGE IIA                2                 6
  STAGE IIA1               4                 1
  STAGE IIA2               2                 5
  STAGE IIB               19                25
  STAGE III                0                 1
  STAGE IIIA               2                 1
  STAGE IIIB              21                21
  STAGE IVA                5                 2
  STAGE IVB                3                 9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    65  23
  4Q LOSS WILD-TYPE 146  44
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               88               190 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               23                44 
$`4Q LOSS MUTATED`
TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 
       17.52        49.48        23.67        11.44         5.46        31.40 
TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A1ML TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       35.01        35.61        20.91        73.18        73.45        83.05 
TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
       18.02        15.48        20.35       147.35        17.19       131.11 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8ZZ 
        9.34        13.61         2.73        99.91        27.52        20.91 
TCGA-DG-A2KJ TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A411 
       95.11        63.98        87.75        39.55        40.87        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       31.73        26.01        14.89        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 
       60.72        26.27         1.51         0.39         0.59         0.36 
TCGA-EK-A2R8 TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A3GM TCGA-EX-A1H5 TCGA-EX-A3L1 
        1.45         0.43         0.53         0.76        20.35        15.22 
TCGA-FU-A3NI TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-JW-A5VK TCGA-JX-A5QV 
       20.98        10.55        17.75        21.67        20.48        20.91 
TCGA-LP-A4AU TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 
       11.28        19.56        11.38        17.23         2.96        16.41 
TCGA-Q1-A73S TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       22.62        11.67        12.16        10.03        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QF TCGA-VS-A8QM 
       32.42        23.97        19.96        32.15        59.18        31.27 
TCGA-VS-A94W TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A959 
       40.87         4.73        40.14        15.68        55.50        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UL TCGA-VS-A9UO TCGA-VS-A9UT TCGA-VS-A9V2 
       50.47        43.40        14.53        47.87        15.85        18.25 
TCGA-VS-A9V4 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-AAXA 
        4.34        26.01        67.59         1.41 

$`4Q LOSS WILD-TYPE`
TCGA-4J-AA1J TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       17.82        57.04        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      177.04       173.29        82.85        19.86        67.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK 
       30.21        57.73        53.16        38.99         0.46         2.43 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       40.93         3.58        44.22        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       33.24        52.01        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8XH 
      101.82       134.33       155.77        94.95        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A907 TCGA-DG-A2KH 
        8.35       146.86        23.51        20.81        14.73         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       82.06        44.94        58.88        36.76        55.63        69.96 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       95.67        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       36.89        26.40         0.30        24.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2IP 
       25.91        27.29        27.25        27.22        24.00         6.64 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
       19.27         0.43         0.13        40.96         4.31         0.10 
TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 
       47.77         0.10         0.49         0.03         7.92        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         8.32        15.55         1.22        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       16.11        31.36        36.26        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC 
       28.31        14.01        35.44         1.12        25.41        16.57 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        24.56        21.44        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AW 
        8.28        18.15        21.11       209.59        44.61         0.89 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y 
       12.49         0.30         0.82        13.35        22.52        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         8.35         8.52        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       54.81        35.05        20.84        15.58        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EL TCGA-VS-A8Q9 
       19.59        14.60        93.99        69.50        65.49        53.59 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       36.13        11.51        39.78        16.64        33.37        58.45 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       56.35        50.14        48.39        28.50        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UP 
       24.30        46.92        45.11         1.71        27.25        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.52        26.07        14.53         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ 
       18.84         5.16        17.75        16.24        15.42        29.26 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         0.16         3.91 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.36              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           147.35            210.67 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           20.695            24.920 
[1] "0.4 - 147.3 (20.7)" "0.0 - 210.7 (24.9)"
[1] "hr=" "1.3"
D49V2, continuous
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED   39 17 11  3
  4Q LOSS WILD-TYPE 96 53 10  5
D49V3, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              39                96
  T2              17                53
  T3              11                10
  T4               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   30 22
  4Q LOSS WILD-TYPE 99 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     30   22
  4Q LOSS WILD-TYPE   99   34
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              30                99
  1              22                34
[1] 2 2
[1] FALSE
D49V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   34  5
  4Q LOSS WILD-TYPE 74  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     34    5
  4Q LOSS WILD-TYPE   74    5
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              34                74
  1               5                 5
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    8 49
  4Q LOSS WILD-TYPE 47 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8   49
  4Q LOSS WILD-TYPE   47   74
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                8                47
  YES              49                74
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED               2                               82
  4Q LOSS WILD-TYPE             4                              160
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4Q LOSS MUTATED                                               2
  4Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4Q LOSS MUTATED                                     2
  4Q LOSS WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4Q LOSS MUTATED                                           1
  4Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4Q LOSS MUTATED                                              4
  4Q LOSS WILD-TYPE                                           13
D49V7, multiclass
                                               clus
vv                                              4Q LOSS MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                           82
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                4
                                               clus
vv                                              4Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            160
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, continuous
D49V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  1     5
  4Q LOSS WILD-TYPE                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED                          12
  4Q LOSS WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           0    65
  4Q LOSS WILD-TYPE                                         2   137
D49V10, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   5                14
  BLACK OR AFRICAN AMERICAN                              12                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  65               137
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     4  51
  4Q LOSS WILD-TYPE  19 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4   51
  4Q LOSS WILD-TYPE   19  111
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                19
  NOT HISPANIC OR LATINO              51               111
[1] 2 2
[1] FALSE
D49V12, continuous
D49V13, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    54  26
  4Q LOSS WILD-TYPE 129  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     54   26
  4Q LOSS WILD-TYPE  129   48
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  TUMOR FREE              54               129
  WITH TUMOR              26                48
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  4Q LOSS MUTATED    1 32 51  0  8
  4Q LOSS WILD-TYPE 17 97 64  1 16
D49V14, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  G1               1                17
  G2              32                97
  G3              51                64
  G4               0                 1
  GX               8                16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, continuous
D49V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4Q LOSS MUTATED                                             8
  4Q LOSS WILD-TYPE                                          30
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  4Q LOSS MUTATED                                        3
  4Q LOSS WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  4Q LOSS MUTATED                                                 1
  4Q LOSS WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4Q LOSS MUTATED               22                  37
  4Q LOSS WILD-TYPE             40                 106
D49V17, multiclass
                                                 clus
vv                                                4Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               22
  LIFELONG NON-SMOKER                                          37
                                                 clus
vv                                                4Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 40
  LIFELONG NON-SMOKER                                           106
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V18, continuous
D49V19, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    9  2
  4Q LOSS WILD-TYPE 16  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9    2
  4Q LOSS WILD-TYPE   16    1
                         clus
vv                        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  9                16
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
D49V20, continuous
D49V21, continuous
D49V22, continuous
D49V23, continuous
D49V24, continuous
D49V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  4Q LOSS MUTATED                                     1
  4Q LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  4Q LOSS MUTATED                                     4                       9
  4Q LOSS WILD-TYPE                                   3                      27
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4Q LOSS MUTATED                         0                       1
  4Q LOSS WILD-TYPE                       1                       7
D49V26, multiclass
                                     clus
vv                                    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               4                 3
  OTHER LOCATION, SPECIFY                           9                27
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  4Q LOSS MUTATED                                               0
  4Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  4Q LOSS MUTATED                                                9
  4Q LOSS WILD-TYPE                                             16
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4Q LOSS MUTATED                                                                                  26
  4Q LOSS WILD-TYPE                                                                                56
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4Q LOSS MUTATED                                                                                             36
  4Q LOSS WILD-TYPE                                                                                           85
D49V27, multiclass
                                                                                              clus
vv                                                                                             4Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              36
                                                                                              clus
vv                                                                                             4Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              16
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V28, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   17 23
  4Q LOSS WILD-TYPE 54 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     17   23
  4Q LOSS WILD-TYPE   54   51
         clus
vv        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ABSENT               17                54
  PRESENT              23                51
[1] 2 2
[1] FALSE
D49V29, continuous
D49V30, continuous
D49V31, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   14 39
  4Q LOSS WILD-TYPE 35 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     14   39
  4Q LOSS WILD-TYPE   35   78
                                          clus
vv                                         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  14                35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              39                78
[1] 2 2
[1] FALSE
D49V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4Q LOSS MUTATED              5          15         28
  4Q LOSS WILD-TYPE           10          39         57
D49V33, multiclass
              clus
vv             4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CURRENT USER               5                10
  FORMER USER               15                39
  NEVER USED                28                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V34, continuous
D49V35, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   21  5
  4Q LOSS WILD-TYPE 71 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     21    5
  4Q LOSS WILD-TYPE   71   13
         clus
vv        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ABSENT               21                71
  PRESENT               5                13
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  4Q LOSS MUTATED             1        38     1
  4Q LOSS WILD-TYPE           4        62     1
D49V36, multiclass
             clus
vv            4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                38                62
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V37, continuous
D49V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  4Q LOSS MUTATED         0        0         0         1       11        22
  4Q LOSS WILD-TYPE       5        1         1         0       23        55
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  4Q LOSS MUTATED          13        0         2          2          0
  4Q LOSS WILD-TYPE        24        4         6          3          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  4Q LOSS MUTATED          16         0          1         16         2
  4Q LOSS WILD-TYPE        28         1          2         26         5
                   vv
clus                STAGE IVB
  4Q LOSS MUTATED           3
  4Q LOSS WILD-TYPE         9
D49V39, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                11                23
  STAGE IB1               22                55
  STAGE IB2               13                24
  STAGE II                 0                 4
  STAGE IIA                2                 6
  STAGE IIA1               2                 3
  STAGE IIA2               0                 7
  STAGE IIB               16                28
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB              16                26
  STAGE IVA                2                 5
  STAGE IVB                3                 9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     9   8
  5P LOSS WILD-TYPE 202  59
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               17               261 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8                59 
$`5P LOSS MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A7CH 
       11.44        68.84        35.01        38.99        35.61       154.32 
TCGA-C5-A7UC TCGA-DS-A0VK TCGA-EA-A556 TCGA-EA-A97N TCGA-EK-A2RK TCGA-FU-A3HY 
       17.19        36.76        14.89         0.36         0.43        31.36 
TCGA-LP-A4AW TCGA-MY-A913 TCGA-VS-A8EH TCGA-VS-A8QH TCGA-VS-A9UU 
        0.89        17.23        32.42        39.78        14.53 

$`5P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF 
       17.52        17.82        49.48        57.04        23.67        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
       19.86        67.46        31.40        46.32        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16         0.46         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      210.67       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
      155.77       131.11        94.95         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
       50.99        45.83         8.35       146.86        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52        20.81        20.91        14.73         1.12        95.11 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       82.06        44.94        63.98        87.75        58.88        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       69.96        95.67        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       31.73        26.01         0.30        24.82         7.46        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI 
       12.59        60.72        26.27         6.64         1.51        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ 
       40.96         4.31         0.10        47.77         0.53         0.10 
TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.49         0.76         0.03        20.35         7.92        15.22 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       14.70        19.79         8.32        15.55         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
       19.04        16.11        36.26        20.98        26.14         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       17.75        25.41        16.57        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       18.15        21.11       209.59        44.61        20.91        11.28 
TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       12.49         0.30         0.82        13.35        22.52        19.56 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         8.35         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
       14.60        11.67        93.99        12.16        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       46.52        45.57        23.97        19.96        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W 
       53.59        36.13        11.51        59.18        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       16.64         4.73        33.37        40.14        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       56.35        55.50        50.14        51.32        50.47        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       48.39        28.50        29.95        27.12        24.30        46.92 
TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       45.11         1.71        14.53        27.25        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.52        26.07        15.85         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.84         5.16        18.25        17.75         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.36              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           154.32            210.67 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            31.36             22.98 
[1] "0.4 - 154.3 (31.4)" "0.0 - 210.7 (23.0)"
[1] "hr=" "2.2"
D50V2, continuous
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED    10   1   3   0
  5P LOSS WILD-TYPE 125  69  18   8
D50V3, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              10               125
  T2               1                69
  T3               3                18
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     6   7
  5P LOSS WILD-TYPE 123  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    7
  5P LOSS WILD-TYPE  123   49
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               6               123
  1               7                49
[1] 2 2
[1] FALSE
D50V5, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    9  1
  5P LOSS WILD-TYPE 99  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      9    1
  5P LOSS WILD-TYPE   99    9
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               9                99
  1               1                 9
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3   5
  5P LOSS WILD-TYPE  52 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3    5
  5P LOSS WILD-TYPE   52  118
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                3                52
  YES               5               118
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED               0                               16
  5P LOSS WILD-TYPE             6                              226
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5P LOSS MUTATED                                               0
  5P LOSS WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5P LOSS MUTATED                                     1
  5P LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5P LOSS MUTATED                                           1
  5P LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5P LOSS MUTATED                                              1
  5P LOSS WILD-TYPE                                           16
D50V7, multiclass
                                               clus
vv                                              5P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           16
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              5P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            226
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, continuous
D50V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     1
  5P LOSS WILD-TYPE                                8    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED                           2
  5P LOSS WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           0    14
  5P LOSS WILD-TYPE                                         2   188
D50V10, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               2                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  14               188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1  13
  5P LOSS WILD-TYPE  22 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   13
  5P LOSS WILD-TYPE   22  149
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                22
  NOT HISPANIC OR LATINO              13               149
[1] 2 2
[1] FALSE
D50V12, continuous
D50V13, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     9   8
  5P LOSS WILD-TYPE 174  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      9    8
  5P LOSS WILD-TYPE  174   66
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  TUMOR FREE               9               174
  WITH TUMOR               8                66
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  5P LOSS MUTATED     2   8   9   0   0
  5P LOSS WILD-TYPE  16 121 106   1  24
D50V14, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  G1               2                16
  G2               8               121
  G3               9               106
  G4               0                 1
  GX               0                24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V15, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                41 
       TCGA-2W-A8YY        TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-C5-A1BQ        TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A2M2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-C5-A8XH 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-C5-A907        TCGA-DG-A2KK        TCGA-DS-A3LQ        TCGA-EK-A2RA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EX-A69M        TCGA-FU-A2QG        TCGA-FU-A3TX        TCGA-FU-A3WB 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-HM-A4S6        TCGA-IR-A3L7        TCGA-IR-A3LB 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-JX-A3Q0        TCGA-MA-AA43        TCGA-MU-A5YI 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-Q1-A73S        TCGA-RA-A741 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-VS-A8QF        TCGA-VS-A94Z        TCGA-VS-A9V0        TCGA-VS-A9V4 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-WL-A834        TCGA-ZJ-A8QR        TCGA-ZJ-AAX4        TCGA-ZJ-AAXA 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ZJ-AB0I 
"5P LOSS WILD-TYPE" 
D50V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5P LOSS MUTATED                                             2
  5P LOSS WILD-TYPE                                          36
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  5P LOSS MUTATED                                        2
  5P LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  5P LOSS MUTATED                                                 1
  5P LOSS WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5P LOSS MUTATED                5                   6
  5P LOSS WILD-TYPE             57                 137
D50V17, multiclass
                                                 clus
vv                                                5P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                5
  LIFELONG NON-SMOKER                                           6
                                                 clus
vv                                                5P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 57
  LIFELONG NON-SMOKER                                           137
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V18, continuous
D50V19, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    4  1
  5P LOSS WILD-TYPE 21  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    1
  5P LOSS WILD-TYPE   21    2
                         clus
vv                        5P LOSS MUTATED 5P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  4                21
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D50V20, continuous
D50V21, continuous
D50V22, continuous
D50V23, continuous
D50V24, continuous
D50V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  5P LOSS MUTATED                                     0
  5P LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  5P LOSS MUTATED                                     1                       3
  5P LOSS WILD-TYPE                                   6                      33
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5P LOSS MUTATED                         0                       1
  5P LOSS WILD-TYPE                       1                       7
D50V26, multiclass
                                     clus
vv                                    5P LOSS MUTATED 5P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 6
  OTHER LOCATION, SPECIFY                           3                33
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  5P LOSS MUTATED                                               0
  5P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5P LOSS MUTATED                                                3
  5P LOSS WILD-TYPE                                             22
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5P LOSS MUTATED                                                                                   4
  5P LOSS WILD-TYPE                                                                                78
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5P LOSS MUTATED                                                                                              8
  5P LOSS WILD-TYPE                                                                                          113
D50V27, multiclass
                                                                                              clus
vv                                                                                             5P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               8
                                                                                              clus
vv                                                                                             5P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           78
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V28, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  7
  5P LOSS WILD-TYPE 69 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    7
  5P LOSS WILD-TYPE   69   67
         clus
vv        5P LOSS MUTATED 5P LOSS WILD-TYPE
  ABSENT                2                69
  PRESENT               7                67
[1] 2 2
[1] FALSE
D50V29, continuous
D50V30, continuous
D50V31, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5   6
  5P LOSS WILD-TYPE  44 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    6
  5P LOSS WILD-TYPE   44  111
                                          clus
vv                                         5P LOSS MUTATED 5P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               6               111
[1] 2 2
[1] FALSE
D50V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5P LOSS MUTATED              1           2          4
  5P LOSS WILD-TYPE           14          52         81
D50V33, multiclass
              clus
vv             5P LOSS MUTATED 5P LOSS WILD-TYPE
  CURRENT USER               1                14
  FORMER USER                2                52
  NEVER USED                 4                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V34, continuous
D50V35, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    6  1
  5P LOSS WILD-TYPE 86 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    1
  5P LOSS WILD-TYPE   86   17
         clus
vv        5P LOSS MUTATED 5P LOSS WILD-TYPE
  ABSENT                6                86
  PRESENT               1                17
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  5P LOSS MUTATED             0         7     1
  5P LOSS WILD-TYPE           5        93     1
D50V36, multiclass
             clus
vv            5P LOSS MUTATED 5P LOSS WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                 7                93
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V37, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                15 
       TCGA-C5-A1BN        TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A1MP 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-ZX-AA5X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D50V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  5P LOSS MUTATED         0        1         0         1        3         4
  5P LOSS WILD-TYPE       5        0         1         0       31        73
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  5P LOSS MUTATED           4        0         1          0          0
  5P LOSS WILD-TYPE        33        4         7          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  5P LOSS MUTATED           2         0          0          3         0
  5P LOSS WILD-TYPE        42         1          3         39         7
                   vv
clus                STAGE IVB
  5P LOSS MUTATED           0
  5P LOSS WILD-TYPE        12
D50V39, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 1                 0
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                 3                31
  STAGE IB1                4                73
  STAGE IB2                4                33
  STAGE II                 0                 4
  STAGE IIA                1                 7
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                2                42
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               3                39
  STAGE IVA                0                 7
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    33  16
  5Q LOSS WILD-TYPE 178  51
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               49               229 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               16                51 
$`5Q LOSS MUTATED`
TCGA-4J-AA1J TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M9 
       17.82        11.44        68.84       144.16         5.46        35.01 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UE 
       38.99        35.61        18.02       154.32        17.19       155.77 
TCGA-C5-A8XH TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A1QT 
       45.83        87.75        36.76        55.63        69.96        40.87 
TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A97N 
       30.90        24.56        31.73        14.89        27.22         0.36 
TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2RK TCGA-EK-A3GK TCGA-FU-A23L TCGA-FU-A2QG 
        6.64         0.43         0.43         0.49        23.84        19.04 
TCGA-FU-A3HY TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-JW-A5VI TCGA-LP-A4AW 
       31.36        10.55        25.41        21.67        24.56         0.89 
TCGA-MA-AA3Z TCGA-MY-A913 TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A8QH 
       19.56        17.23        32.42        19.96        59.18        39.78 
TCGA-VS-A94Y TCGA-VS-A9U5 TCGA-VS-A9UU TCGA-VS-A9V4 TCGA-WL-A834 TCGA-XS-A8TJ 
        4.73        50.47        14.53         4.34        26.01        29.26 
TCGA-ZJ-A8QR 
       19.13 

$`5Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BI 
       17.52        49.48        57.04        23.67        18.74        36.56 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04       173.29        82.85        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK 
       46.32        30.21        57.73        53.16         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       210.67       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       20.35       147.35       131.11        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
        2.73        50.99         8.35       146.86        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52        20.81        20.91        14.73         1.12        95.11 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A3LQ 
       82.06        44.94        63.98        58.88        95.67        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       16.83        16.18        17.52         8.28        39.55        37.35 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       26.01         0.30        24.82         7.46        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       27.29        27.25        24.00        13.48        12.59        60.72 
TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 
       26.27         1.51        19.27         0.39         0.59         0.36 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL 
        1.45         0.13        40.96         4.31         0.10        47.77 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.53         0.10         0.76         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       15.22        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       16.11        36.26        20.98        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC 
       28.31        14.01        35.44         1.12        17.75        16.57 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       27.42         3.29        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        8.28        18.15        21.11       209.59        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
       11.28        12.49         0.30         0.82        13.35        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       19.56        17.82         8.35         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       34.62        19.96        54.81        35.05        20.84         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB 
       14.60        11.67        93.99        12.16        69.50        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       46.52        45.57        23.97        65.49        32.15        53.59 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z 
       36.13        11.51        31.27        40.87        16.64        33.37 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       40.14        58.45        15.68        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       51.32        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       24.30        46.92        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV 
       47.87        47.47        41.52        26.07        15.85         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       16.24        15.42        67.59         0.69         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.36              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           155.77            210.67 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            24.56             22.52 
[1] "0.4 - 155.8 (24.6)" "0.0 - 210.7 (22.5)"
[1] "hr=" "1.5"
D51V2, continuous
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED    29   8   2   1
  5Q LOSS WILD-TYPE 106  62  19   7
D51V3, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              29               106
  T2               8                62
  T3               2                19
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    22  11
  5Q LOSS WILD-TYPE 107  45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     22   11
  5Q LOSS WILD-TYPE  107   45
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              22               107
  1              11                45
[1] 2 2
[1] FALSE
D51V5, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   21  2
  5Q LOSS WILD-TYPE 87  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     21    2
  5Q LOSS WILD-TYPE   87    8
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              21                87
  1               2                 8
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     9  17
  5Q LOSS WILD-TYPE  46 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      9   17
  5Q LOSS WILD-TYPE   46  106
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                9                46
  YES              17               106
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED               0                               46
  5Q LOSS WILD-TYPE             6                              196
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5Q LOSS MUTATED                                               0
  5Q LOSS WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5Q LOSS MUTATED                                     2
  5Q LOSS WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5Q LOSS MUTATED                                           1
  5Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5Q LOSS MUTATED                                              2
  5Q LOSS WILD-TYPE                                           15
D51V7, multiclass
                                               clus
vv                                              5Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           46
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              5Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            196
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, continuous
D51V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     4
  5Q LOSS WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED                           4
  5Q LOSS WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           1    39
  5Q LOSS WILD-TYPE                                         1   163
D51V10, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                               4                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 1
  WHITE                                                  39               163
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     4  31
  5Q LOSS WILD-TYPE  19 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4   31
  5Q LOSS WILD-TYPE   19  131
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                19
  NOT HISPANIC OR LATINO              31               131
[1] 2 2
[1] FALSE
D51V12, continuous
D51V13, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    28  17
  5Q LOSS WILD-TYPE 155  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     28   17
  5Q LOSS WILD-TYPE  155   57
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  TUMOR FREE              28               155
  WITH TUMOR              17                57
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  5Q LOSS MUTATED     2  19  25   0   3
  5Q LOSS WILD-TYPE  16 110  90   1  21
D51V14, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  G1               2                16
  G2              19               110
  G3              25                90
  G4               0                 1
  GX               3                21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, continuous
D51V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5Q LOSS MUTATED                                             7
  5Q LOSS WILD-TYPE                                          31
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  5Q LOSS MUTATED                                        2
  5Q LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  5Q LOSS MUTATED                                                 2
  5Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5Q LOSS MUTATED               12                  20
  5Q LOSS WILD-TYPE             50                 123
D51V17, multiclass
                                                 clus
vv                                                5Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               2
  CURRENT SMOKER                                               12
  LIFELONG NON-SMOKER                                          20
                                                 clus
vv                                                5Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 50
  LIFELONG NON-SMOKER                                           123
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V18, continuous
D51V19, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    7  1
  5Q LOSS WILD-TYPE 18  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    1
  5Q LOSS WILD-TYPE   18    2
                         clus
vv                        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  7                18
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D51V20, continuous
D51V21, continuous
D51V22, continuous
D51V23, continuous
D51V24, continuous
D51V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  5Q LOSS MUTATED                                     0
  5Q LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  5Q LOSS MUTATED                                     2                       8
  5Q LOSS WILD-TYPE                                   5                      28
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5Q LOSS MUTATED                         0                       1
  5Q LOSS WILD-TYPE                       1                       7
D51V26, multiclass
                                     clus
vv                                    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 5
  OTHER LOCATION, SPECIFY                           8                28
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  5Q LOSS MUTATED                                               0
  5Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5Q LOSS MUTATED                                                6
  5Q LOSS WILD-TYPE                                             19
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5Q LOSS MUTATED                                                                                  12
  5Q LOSS WILD-TYPE                                                                                70
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5Q LOSS MUTATED                                                                                             23
  5Q LOSS WILD-TYPE                                                                                           98
D51V27, multiclass
                                                                                              clus
vv                                                                                             5Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              23
                                                                                              clus
vv                                                                                             5Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V28, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    9 19
  5Q LOSS WILD-TYPE 62 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      9   19
  5Q LOSS WILD-TYPE   62   55
         clus
vv        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ABSENT                9                62
  PRESENT              19                55
[1] 2 2
[1] FALSE
D51V29, continuous
D51V30, continuous
D51V31, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    8 25
  5Q LOSS WILD-TYPE 41 92
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8   25
  5Q LOSS WILD-TYPE   41   92
                                          clus
vv                                         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   8                41
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              25                92
[1] 2 2
[1] FALSE
D51V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5Q LOSS MUTATED              3          11         11
  5Q LOSS WILD-TYPE           12          43         74
D51V33, multiclass
              clus
vv             5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CURRENT USER               3                12
  FORMER USER               11                43
  NEVER USED                11                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V34, continuous
D51V35, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   16  4
  5Q LOSS WILD-TYPE 76 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     16    4
  5Q LOSS WILD-TYPE   76   14
         clus
vv        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ABSENT               16                76
  PRESENT               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  5Q LOSS MUTATED             0        18     1
  5Q LOSS WILD-TYPE           5        82     1
D51V36, multiclass
             clus
vv            5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                18                82
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V37, continuous
D51V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  5Q LOSS MUTATED         1        1         0         1        7        13
  5Q LOSS WILD-TYPE       4        0         1         0       27        64
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  5Q LOSS MUTATED          10        1         1          2          0
  5Q LOSS WILD-TYPE        27        3         7          3          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  5Q LOSS MUTATED           8         0          0          4         1
  5Q LOSS WILD-TYPE        36         1          3         38         6
                   vv
clus                STAGE IVB
  5Q LOSS MUTATED           0
  5Q LOSS WILD-TYPE        12
D51V39, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 1                 0
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                 7                27
  STAGE IB1               13                64
  STAGE IB2               10                27
  STAGE II                 1                 3
  STAGE IIA                1                 7
  STAGE IIA1               2                 3
  STAGE IIA2               0                 7
  STAGE IIB                8                36
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               4                38
  STAGE IVA                1                 6
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    35   8
  6P LOSS WILD-TYPE 176  59
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               43               235 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                59 
$`6P LOSS MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A2LT TCGA-C5-A7CG 
       17.82        49.48        19.86        30.21        73.18       210.67 
TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8YQ TCGA-C5-A8YR 
      147.35       131.11         9.34        50.99        23.51        27.52 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DS-A0VK TCGA-EA-A3QE 
        1.12        95.11        44.94        63.98        36.76        25.02 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PI 
        0.30        14.89        24.00        12.59         1.51        19.27 
TCGA-EK-A2RC TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-FU-A3HY TCGA-IR-A3L7 
        4.31         0.53         0.10         7.92        31.36       147.39 
TCGA-JW-A5VJ TCGA-JX-A5QV TCGA-MA-AA42 TCGA-Q1-A6DT TCGA-VS-A8EL TCGA-VS-A8QC 
       21.44        20.91         8.52         9.04        65.49        11.51 
TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A957 TCGA-VS-A9U5 TCGA-VS-A9UC TCGA-VS-A9UU 
       59.18         4.73        55.50        50.47        27.12        14.53 
TCGA-VS-A9V3 
       17.75 

$`6P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       17.52        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        31.40        46.32        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN 
       38.99        35.61         0.46         2.43        20.91        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
        3.58        44.22        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC 
      154.32       101.82       134.33        15.48        20.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XI 
      155.77        94.95        13.61         2.73        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK 
      146.86        99.91        20.81        20.91        14.73        82.06 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       87.75        58.88        55.63        69.96        95.67        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18        17.52         8.28        39.55        40.87 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 
       37.35        30.90        31.53        31.36        13.05        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        31.73        26.01        24.82         7.46 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R 
       26.79        25.91        27.29        27.25        27.22        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL 
        0.36        60.72        26.27         6.64         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD 
        0.59         0.36         1.45         0.13        40.96         0.10 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
        0.43        47.77         0.49         0.76         0.03        20.35 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       15.22        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       23.84        19.04        16.11        36.26        20.98        26.14 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12        17.75        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        44.61        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        19.56        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         8.35        11.38        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
       54.81        35.05        20.84        17.23         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       16.41        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        69.50        10.03        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       32.42        23.97        19.96        32.15        53.59        36.13 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 
       39.78        31.27        40.87        16.64        33.37        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 
       58.45        15.68        56.35        50.14        51.32        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
       48.39        28.50        29.95        24.30        46.92        45.11 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
        1.71        14.53        27.25        47.87        47.47        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       26.07        15.85         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
        5.16        18.25         4.34        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       29.26        67.59        19.13         0.69         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.10              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           210.67            209.59 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            23.51             22.98 
[1] "0.1 - 210.7 (23.5)" "0.0 - 209.6 (23.0)"
[1] "hr=" "1.4"
D52V2, continuous
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED    20  12   0   1
  6P LOSS WILD-TYPE 115  58  21   7
D52V3, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              20               115
  T2              12                58
  T3               0                21
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    16   9
  6P LOSS WILD-TYPE 113  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     16    9
  6P LOSS WILD-TYPE  113   47
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              16               113
  1               9                47
[1] 2 2
[1] FALSE
D52V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   20  0
  6P LOSS WILD-TYPE 88 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     20    0
  6P LOSS WILD-TYPE   88   10
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              20                88
  1               0                10
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     8  18
  6P LOSS WILD-TYPE  47 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      8   18
  6P LOSS WILD-TYPE   47  105
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                8                47
  YES              18               105
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED               1                               44
  6P LOSS WILD-TYPE             5                              198
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6P LOSS MUTATED                                               0
  6P LOSS WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6P LOSS MUTATED                                     1
  6P LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6P LOSS MUTATED                                           1
  6P LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6P LOSS MUTATED                                              0
  6P LOSS WILD-TYPE                                           17
D52V7, multiclass
                                               clus
vv                                              6P LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           44
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              6P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            198
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, continuous
D52V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  1     1
  6P LOSS WILD-TYPE                                7    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED                           3
  6P LOSS WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           1    32
  6P LOSS WILD-TYPE                                         1   170
D52V10, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               3                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 1
  WHITE                                                  32               170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2  23
  6P LOSS WILD-TYPE  21 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   23
  6P LOSS WILD-TYPE   21  139
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                21
  NOT HISPANIC OR LATINO              23               139
[1] 2 2
[1] FALSE
D52V12, continuous
D52V13, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    27  11
  6P LOSS WILD-TYPE 156  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     27   11
  6P LOSS WILD-TYPE  156   63
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  TUMOR FREE              27               156
  WITH TUMOR              11                63
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  6P LOSS MUTATED     3  17  22   0   3
  6P LOSS WILD-TYPE  15 112  93   1  21
D52V14, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  G1               3                15
  G2              17               112
  G3              22                93
  G4               0                 1
  GX               3                21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, continuous
D52V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6P LOSS MUTATED                                             6
  6P LOSS WILD-TYPE                                          32
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  6P LOSS MUTATED                                        1
  6P LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  6P LOSS MUTATED                                                 0
  6P LOSS WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6P LOSS MUTATED               10                  20
  6P LOSS WILD-TYPE             52                 123
D52V17, multiclass
                                                 clus
vv                                                6P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               10
  LIFELONG NON-SMOKER                                          20
                                                 clus
vv                                                6P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 52
  LIFELONG NON-SMOKER                                           123
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V18, continuous
D52V19, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    2  0
  6P LOSS WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    0
  6P LOSS WILD-TYPE   23    3
                         clus
vv                        6P LOSS MUTATED 6P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  2                23
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D52V20, continuous
D52V21, continuous
D52V22, continuous
D52V23, continuous
D52V24, continuous
D52V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  6P LOSS MUTATED                                     0
  6P LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  6P LOSS MUTATED                                     0                       5
  6P LOSS WILD-TYPE                                   7                      31
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6P LOSS MUTATED                         0                       2
  6P LOSS WILD-TYPE                       1                       6
D52V26, multiclass
                                     clus
vv                                    6P LOSS MUTATED 6P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           5                31
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  6P LOSS MUTATED                                               1
  6P LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  6P LOSS MUTATED                                                4
  6P LOSS WILD-TYPE                                             21
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6P LOSS MUTATED                                                                                  12
  6P LOSS WILD-TYPE                                                                                70
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6P LOSS MUTATED                                                                                             15
  6P LOSS WILD-TYPE                                                                                          106
D52V27, multiclass
                                                                                              clus
vv                                                                                             6P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              15
                                                                                              clus
vv                                                                                             6P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V28, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    9 10
  6P LOSS WILD-TYPE 62 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9   10
  6P LOSS WILD-TYPE   62   64
         clus
vv        6P LOSS MUTATED 6P LOSS WILD-TYPE
  ABSENT                9                62
  PRESENT              10                64
[1] 2 2
[1] FALSE
D52V29, continuous
D52V30, continuous
D52V31, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     9  15
  6P LOSS WILD-TYPE  40 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9   15
  6P LOSS WILD-TYPE   40  102
                                          clus
vv                                         6P LOSS MUTATED 6P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   9                40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              15               102
[1] 2 2
[1] FALSE
D52V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6P LOSS MUTATED              4           6         13
  6P LOSS WILD-TYPE           11          48         72
D52V33, multiclass
              clus
vv             6P LOSS MUTATED 6P LOSS WILD-TYPE
  CURRENT USER               4                11
  FORMER USER                6                48
  NEVER USED                13                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V34, continuous
D52V35, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   16  1
  6P LOSS WILD-TYPE 76 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     16    1
  6P LOSS WILD-TYPE   76   17
         clus
vv        6P LOSS MUTATED 6P LOSS WILD-TYPE
  ABSENT               16                76
  PRESENT               1                17
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  6P LOSS MUTATED             0        17     0
  6P LOSS WILD-TYPE           5        83     2
D52V36, multiclass
             clus
vv            6P LOSS MUTATED 6P LOSS WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                17                83
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V37, continuous
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
D52V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  6P LOSS MUTATED         1        0         0         0        6        13
  6P LOSS WILD-TYPE       4        1         1         1       28        64
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  6P LOSS MUTATED           4        0         1          0          0
  6P LOSS WILD-TYPE        33        4         7          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  6P LOSS MUTATED           9         0          0          9         1
  6P LOSS WILD-TYPE        35         1          3         33         6
                   vv
clus                STAGE IVB
  6P LOSS MUTATED           1
  6P LOSS WILD-TYPE        11
D52V39, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 6                28
  STAGE IB1               13                64
  STAGE IB2                4                33
  STAGE II                 0                 4
  STAGE IIA                1                 7
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                9                35
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               9                33
  STAGE IVA                1                 6
  STAGE IVB                1                11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    55  11
  6Q LOSS WILD-TYPE 156  56
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               66               212 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               11                56 
$`6Q LOSS MUTATED`
TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BI TCGA-C5-A1BL TCGA-C5-A1BM 
       17.82        49.48        23.67        36.56       173.29        82.85 
TCGA-C5-A1M8 TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CO 
       30.21        73.18        73.45       210.67       154.32       147.35 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8YQ TCGA-C5-A8YR 
      131.11        94.95         9.34        50.99        23.51        27.52 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM TCGA-EA-A1QT TCGA-EA-A3QE 
        1.12        95.11        44.94        63.98        40.87        25.02 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2PG 
        0.30        14.89        27.22        24.00        12.59         1.51 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2RC TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GM 
       19.27         0.39         4.31         0.53         0.10         0.76 
TCGA-EX-A1H6 TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        7.92        23.84        31.36        28.31        14.01        35.44 
TCGA-IR-A3L7 TCGA-JW-A5VJ TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-LP-A4AX TCGA-MA-AA42 
      147.39        21.44        21.11        20.91        12.49         8.52 
TCGA-MU-A5YI TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-VS-A8EB TCGA-VS-A8EL TCGA-VS-A8QC 
       34.62        16.41         9.04        10.03        65.49        11.51 
TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       59.18         4.73        40.14        55.50        51.32        50.47 
TCGA-VS-A9UC TCGA-VS-A9UU TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
       27.12        14.53        18.25        17.75        29.26        19.13 

$`6Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ 
       17.52        57.04        11.44        68.84        18.74       144.16 
TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
      177.04         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       35.01        57.73        53.16        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX 
        2.43        20.91        40.93         3.58        44.22        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       17.85        20.42       101.82       134.33        15.48        20.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XI 
       17.19       155.77        13.61         2.73        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KK 
      146.86        99.91        20.81        20.91        14.73        82.06 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76        55.63        69.96        95.67 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 
       37.35        30.90        31.53        31.36        13.05        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        31.73        26.01        24.82         7.46 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A78R TCGA-EA-A97N 
       26.79        25.91        27.29        27.25        13.48         0.36 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
       60.72        26.27         6.64         0.43         0.59         0.36 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL 
        1.45         0.13        40.96         0.10         0.43        47.77 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.49         0.03        20.35        15.22        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
        8.32        15.55         1.22        19.04        16.11        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A5XV TCGA-FU-A770 
       20.98        26.14         1.48        16.14        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       17.75        25.41        16.57        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
        9.44       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 
       20.48        15.58        28.37         8.28        18.15       209.59 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       44.61        11.28         0.89         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 
       22.52        19.56        17.82        19.56         8.35        11.38 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       28.08        19.96        54.81        35.05        20.84        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
        2.96        15.58        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG 
       11.67        93.99        12.16        69.50        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       32.42        23.97        19.96        32.15        53.59        36.13 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        40.87        16.64        33.37        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       15.68        56.35        50.14        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       29.95        24.30        46.92        45.11         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       27.25        47.87        47.47        41.52        26.07        15.85 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V4 
        3.42        18.25        67.20        18.84         5.16         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       16.24        15.42        26.01        67.59         0.69         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.10              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           210.67            209.59 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           24.510            21.325 
[1] "0.1 - 210.7 (24.5)" "0.0 - 209.6 (21.3)"
[1] "hr=" "1.8"
D53V2, continuous
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED    32  16   4   1
  6Q LOSS WILD-TYPE 103  54  17   7
D53V3, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              32               103
  T2              16                54
  T3               4                17
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    26  14
  6Q LOSS WILD-TYPE 103  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     26   14
  6Q LOSS WILD-TYPE  103   42
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              26               103
  1              14                42
[1] 2 2
[1] FALSE
D53V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   28  1
  6Q LOSS WILD-TYPE 80  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     28    1
  6Q LOSS WILD-TYPE   80    9
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              28                80
  1               1                 9
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   15 24
  6Q LOSS WILD-TYPE 40 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15   24
  6Q LOSS WILD-TYPE   40   99
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               15                40
  YES              24                99
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED               1                               67
  6Q LOSS WILD-TYPE             5                              175
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6Q LOSS MUTATED                                               1
  6Q LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6Q LOSS MUTATED                                     4
  6Q LOSS WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6Q LOSS MUTATED                                           1
  6Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6Q LOSS MUTATED                                              0
  6Q LOSS WILD-TYPE                                           17
D53V7, multiclass
                                               clus
vv                                              6Q LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           67
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              6Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            175
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 17
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, continuous
D53V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  1     3
  6Q LOSS WILD-TYPE                                7    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED                           8
  6Q LOSS WILD-TYPE                        20
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           2    48
  6Q LOSS WILD-TYPE                                         0   154
D53V10, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               8                20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 0
  WHITE                                                  48               154
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     4  40
  6Q LOSS WILD-TYPE  19 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4   40
  6Q LOSS WILD-TYPE   19  122
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                19
  NOT HISPANIC OR LATINO              40               122
[1] 2 2
[1] FALSE
D53V12, continuous
D53V13, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    43  15
  6Q LOSS WILD-TYPE 140  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     43   15
  6Q LOSS WILD-TYPE  140   59
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  TUMOR FREE              43               140
  WITH TUMOR              15                59
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  6Q LOSS MUTATED     4  29  33   0   5
  6Q LOSS WILD-TYPE  14 100  82   1  19
D53V14, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  G1               4                14
  G2              29               100
  G3              33                82
  G4               0                 1
  GX               5                19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V15, continuous
D53V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6Q LOSS MUTATED                                             7
  6Q LOSS WILD-TYPE                                          31
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  6Q LOSS MUTATED                                        2
  6Q LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  6Q LOSS MUTATED                                                 1
  6Q LOSS WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6Q LOSS MUTATED               17                  34
  6Q LOSS WILD-TYPE             45                 109
D53V17, multiclass
                                                 clus
vv                                                6Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               17
  LIFELONG NON-SMOKER                                          34
                                                 clus
vv                                                6Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 45
  LIFELONG NON-SMOKER                                           109
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V18, continuous
D53V19, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    5  0
  6Q LOSS WILD-TYPE 20  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    0
  6Q LOSS WILD-TYPE   20    3
                         clus
vv                        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D53V20, continuous
D53V21, continuous
D53V22, continuous
D53V23, continuous
D53V24, continuous
D53V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  6Q LOSS MUTATED                                     0
  6Q LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  6Q LOSS MUTATED                                     1                       8
  6Q LOSS WILD-TYPE                                   6                      28
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6Q LOSS MUTATED                         0                       2
  6Q LOSS WILD-TYPE                       1                       6
D53V26, multiclass
                                     clus
vv                                    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 6
  OTHER LOCATION, SPECIFY                           8                28
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  6Q LOSS MUTATED                                               1
  6Q LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  6Q LOSS MUTATED                                                7
  6Q LOSS WILD-TYPE                                             18
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6Q LOSS MUTATED                                                                                  18
  6Q LOSS WILD-TYPE                                                                                64
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6Q LOSS MUTATED                                                                                             25
  6Q LOSS WILD-TYPE                                                                                           96
D53V27, multiclass
                                                                                              clus
vv                                                                                             6Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              25
                                                                                              clus
vv                                                                                             6Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           64
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V28, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   15 16
  6Q LOSS WILD-TYPE 56 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15   16
  6Q LOSS WILD-TYPE   56   58
         clus
vv        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ABSENT               15                56
  PRESENT              16                58
[1] 2 2
[1] FALSE
D53V29, continuous
D53V30, continuous
D53V31, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   10 29
  6Q LOSS WILD-TYPE 39 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     10   29
  6Q LOSS WILD-TYPE   39   88
                                          clus
vv                                         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  10                39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              29                88
[1] 2 2
[1] FALSE
D53V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6Q LOSS MUTATED              4          12         20
  6Q LOSS WILD-TYPE           11          42         65
D53V33, multiclass
              clus
vv             6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CURRENT USER               4                11
  FORMER USER               12                42
  NEVER USED                20                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V34, continuous
D53V35, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   24  4
  6Q LOSS WILD-TYPE 68 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     24    4
  6Q LOSS WILD-TYPE   68   14
         clus
vv        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ABSENT               24                68
  PRESENT               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  6Q LOSS MUTATED             0        20     0
  6Q LOSS WILD-TYPE           5        80     2
D53V36, multiclass
             clus
vv            6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                20                80
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V37, continuous
[1] "Remove cluster labels:" "6Q LOSS MUTATED"       
clus
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
D53V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  6Q LOSS MUTATED         2        0         1         0       10        21
  6Q LOSS WILD-TYPE       3        1         0         1       24        56
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  6Q LOSS MUTATED           6        0         2          1          0
  6Q LOSS WILD-TYPE        31        4         6          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  6Q LOSS MUTATED          11         0          1         13         1
  6Q LOSS WILD-TYPE        33         1          2         29         6
                   vv
clus                STAGE IVB
  6Q LOSS MUTATED           2
  6Q LOSS WILD-TYPE        10
D53V39, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 0                 1
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                10                24
  STAGE IB1               21                56
  STAGE IB2                6                31
  STAGE II                 0                 4
  STAGE IIA                2                 6
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB               11                33
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB              13                29
  STAGE IVA                1                 6
  STAGE IVB                2                10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    15   9
  7P LOSS WILD-TYPE 196  58
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               24               254 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                9                58 
$`7P LOSS MUTATED`
TCGA-C5-A0TN TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       11.44        31.40        35.01        53.16        38.99        35.61 
TCGA-C5-A2LX TCGA-C5-A7CK TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DS-A7WH TCGA-EA-A1QS 
       83.05       134.33        13.61        87.75        17.52        39.55 
TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EX-A1H5 TCGA-JX-A3Q8 TCGA-LP-A7HU 
       31.73        27.22         0.36        20.35        44.61        13.35 
TCGA-RA-A741 TCGA-VS-A957 TCGA-VS-A9UI TCGA-VS-A9UV TCGA-VS-A9V3 TCGA-ZJ-AAXU 
       14.60        55.50        45.11         3.42        17.75         0.16 

$`7P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        23.67        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
        5.46        19.86        67.46        46.32        30.21        57.73 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.18        73.45        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       52.01        18.02        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82        15.48        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
      131.11        94.95         9.34         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35       146.86        99.91        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91        14.73         1.12        95.11        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       63.98        58.88        36.76        55.63        69.96        95.67 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ 
       22.98        16.83        16.18         8.28        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        26.01         0.30        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       14.89        26.79        25.91        27.29        27.25        24.00 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48        12.59        60.72        26.27         6.64         1.51 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
       19.27         0.39         0.43         0.59         0.36         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL 
        0.13        40.96         4.31         0.10         0.43        47.77 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H6 
        0.53         0.10         0.49         0.76         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       15.22        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
       26.14         1.48        16.14        28.31        14.01        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       10.55         1.12        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV 
       28.37         8.28        18.15        21.11       209.59        20.91 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W 
       11.28         0.89        12.49         0.30         0.82        22.52 
TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       19.56        17.82        19.56         8.35         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       28.08        34.62        19.96        54.81        35.05        20.84 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       17.23         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       22.62        19.59        11.67        93.99        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       10.03        46.52        45.57        32.42        23.97        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       65.49        32.15        53.59        36.13        11.51        59.18 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78        31.27        40.87        16.64         4.73        33.37 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 
       40.14        58.45        15.68        56.35        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       50.47        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       24.30        46.92         1.71        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UY 
       47.47        41.52        26.07        15.85        14.53        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-A9V5 
       67.20        18.84         5.16        18.25         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZX-AA5X 
        1.41         3.91 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.16              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           134.33            210.67 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           31.565            22.570 
[1] "0.2 - 134.3 (31.6)" "0.0 - 210.7 (22.6)"
[1] "hr=" "1.5"
D54V2, continuous
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED    11   6   1   2
  7P LOSS WILD-TYPE 124  64  20   6
D54V3, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1              11               124
  T2               6                64
  T3               1                20
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    10   5
  7P LOSS WILD-TYPE 119  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     10    5
  7P LOSS WILD-TYPE  119   51
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              10               119
  1               5                51
[1] 2 2
[1] FALSE
D54V5, binary
                   cls
clus                 0  1
  7P LOSS MUTATED   10  0
  7P LOSS WILD-TYPE 98 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     10    0
  7P LOSS WILD-TYPE   98   10
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0              10                98
  1               0                10
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     4  10
  7P LOSS WILD-TYPE  51 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4   10
  7P LOSS WILD-TYPE   51  113
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                4                51
  YES              10               113
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED               0                               21
  7P LOSS WILD-TYPE             6                              221
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7P LOSS MUTATED                                               1
  7P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7P LOSS MUTATED                                     3
  7P LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7P LOSS MUTATED                                           0
  7P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7P LOSS MUTATED                                              1
  7P LOSS WILD-TYPE                                           16
D54V7, multiclass
                                               clus
vv                                              7P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           21
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              7P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            221
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, continuous
D54V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     5
  7P LOSS WILD-TYPE                                8    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED                           3
  7P LOSS WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           0    17
  7P LOSS WILD-TYPE                                         2   185
D54V10, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   5                14
  BLACK OR AFRICAN AMERICAN                               3                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  17               185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  20
  7P LOSS WILD-TYPE  23 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   20
  7P LOSS WILD-TYPE   23  142
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                23
  NOT HISPANIC OR LATINO              20               142
[1] 2 2
[1] FALSE
D54V12, continuous
D54V13, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    14  10
  7P LOSS WILD-TYPE 169  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     14   10
  7P LOSS WILD-TYPE  169   64
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  TUMOR FREE              14               169
  WITH TUMOR              10                64
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  7P LOSS MUTATED     0   9  14   0   3
  7P LOSS WILD-TYPE  18 120 101   1  21
D54V14, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  G1               0                18
  G2               9               120
  G3              14               101
  G4               0                 1
  GX               3                21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, continuous
D54V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7P LOSS MUTATED                                             2
  7P LOSS WILD-TYPE                                          36
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  7P LOSS MUTATED                                        1
  7P LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  7P LOSS MUTATED                                                 1
  7P LOSS WILD-TYPE                                               2
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7P LOSS MUTATED                4                  16
  7P LOSS WILD-TYPE             58                 127
D54V17, multiclass
                                                 clus
vv                                                7P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                4
  LIFELONG NON-SMOKER                                          16
                                                 clus
vv                                                7P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 2
  CURRENT SMOKER                                                 58
  LIFELONG NON-SMOKER                                           127
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V18, continuous
D54V19, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    7  1
  7P LOSS WILD-TYPE 18  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7    1
  7P LOSS WILD-TYPE   18    2
                         clus
vv                        7P LOSS MUTATED 7P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  7                18
  TREATMENT NOT COMPLETED               1                 2
[1] 2 2
[1] FALSE
D54V20, continuous
D54V21, continuous
D54V22, continuous
D54V23, continuous
D54V24, continuous
D54V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  7P LOSS MUTATED                                     0
  7P LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  7P LOSS MUTATED                                     2                       2
  7P LOSS WILD-TYPE                                   5                      34
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7P LOSS MUTATED                         0                       1
  7P LOSS WILD-TYPE                       1                       7
D54V26, multiclass
                                     clus
vv                                    7P LOSS MUTATED 7P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 5
  OTHER LOCATION, SPECIFY                           2                34
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  7P LOSS MUTATED                                               0
  7P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  7P LOSS MUTATED                                                2
  7P LOSS WILD-TYPE                                             23
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7P LOSS MUTATED                                                                                  10
  7P LOSS WILD-TYPE                                                                                72
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7P LOSS MUTATED                                                                                              8
  7P LOSS WILD-TYPE                                                                                          113
D54V27, multiclass
                                                                                              clus
vv                                                                                             7P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               8
                                                                                              clus
vv                                                                                             7P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           72
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V28, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    6  8
  7P LOSS WILD-TYPE 65 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      6    8
  7P LOSS WILD-TYPE   65   66
         clus
vv        7P LOSS MUTATED 7P LOSS WILD-TYPE
  ABSENT                6                65
  PRESENT               8                66
[1] 2 2
[1] FALSE
D54V29, continuous
D54V30, continuous
D54V31, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     6   9
  7P LOSS WILD-TYPE  43 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      6    9
  7P LOSS WILD-TYPE   43  108
                                          clus
vv                                         7P LOSS MUTATED 7P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               9               108
[1] 2 2
[1] FALSE
D54V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7P LOSS MUTATED              0           8          8
  7P LOSS WILD-TYPE           15          46         77
D54V33, multiclass
              clus
vv             7P LOSS MUTATED 7P LOSS WILD-TYPE
  CURRENT USER               0                15
  FORMER USER                8                46
  NEVER USED                 8                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V34, continuous
D54V35, binary
                   cls
clus                 0  1
  7P LOSS MUTATED   12  1
  7P LOSS WILD-TYPE 80 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     12    1
  7P LOSS WILD-TYPE   80   17
         clus
vv        7P LOSS MUTATED 7P LOSS WILD-TYPE
  ABSENT               12                80
  PRESENT               1                17
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  7P LOSS MUTATED             1         9     0
  7P LOSS WILD-TYPE           4        91     2
D54V36, multiclass
             clus
vv            7P LOSS MUTATED 7P LOSS WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                 9                91
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V37, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2                15 
       TCGA-C5-A1BN        TCGA-C5-A1ML        TCGA-C5-A1MN        TCGA-C5-A1MP 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42        TCGA-MU-A51Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
D54V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  7P LOSS MUTATED         0        0         0         0        2         8
  7P LOSS WILD-TYPE       5        1         1         1       32        69
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  7P LOSS MUTATED           4        1         0          1          0
  7P LOSS WILD-TYPE        33        3         8          4          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  7P LOSS MUTATED           5         0          0          1         2
  7P LOSS WILD-TYPE        39         1          3         41         5
                   vv
clus                STAGE IVB
  7P LOSS MUTATED           2
  7P LOSS WILD-TYPE        10
D54V39, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 2                32
  STAGE IB1                8                69
  STAGE IB2                4                33
  STAGE II                 1                 3
  STAGE IIA                0                 8
  STAGE IIA1               1                 4
  STAGE IIA2               0                 7
  STAGE IIB                5                39
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               1                41
  STAGE IVA                2                 5
  STAGE IVB                2                10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    22  12
  7Q LOSS WILD-TYPE 189  55
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               34               244 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               12                55 
$`7Q LOSS MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI 
       11.44         5.46        31.40        35.01        38.99        35.61 
TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7X5 
       40.93        73.45        83.05       154.32        15.48        13.61 
TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EA-A97N TCGA-EK-A2H0 
       17.52        39.55        31.73        27.22         0.36        60.72 
TCGA-EK-A2H1 TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A2QG TCGA-FU-A40J TCGA-HM-A3JJ 
       26.27         0.49        20.35        19.04        14.01        21.67 
TCGA-JW-A5VG TCGA-JX-A3Q8 TCGA-LP-A7HU TCGA-MY-A5BF TCGA-RA-A741 TCGA-VS-A957 
       27.42        44.61        13.35        20.84        14.60        55.50 
TCGA-VS-A9UO TCGA-VS-A9UV TCGA-VS-A9UY TCGA-ZJ-A8QQ 
       47.87         3.42        18.25        67.59 

$`7Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        23.67        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF 
       19.86        67.46        46.32        30.21        57.73        53.16 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
        0.46         2.43        20.91         3.58        44.22        73.18 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM 
       17.85        20.42       210.67       101.82       134.33        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      147.35        17.19       155.77       131.11        94.95         9.34 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        14.73         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       95.11        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76        55.63        69.96        95.67        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18         8.28        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       26.01         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       25.91        27.29        27.25        24.00        13.48        12.59 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
        6.64         1.51        19.27         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.36         1.45         0.13        40.96         4.31         0.10 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GM TCGA-EK-A3GN 
        0.43        47.77         0.53         0.10         0.76         0.03 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        7.92        15.22        14.70        19.79         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22        23.84        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
       26.14         1.48        16.14        28.31        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
        1.12        17.75        25.41        16.57        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        29.85        36.36         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        20.91        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.30         0.82        22.52        19.56        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        8.35         8.52        11.38        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       54.81        35.05        17.23         2.96        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF 
        9.34        18.64        22.62        19.59        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       23.97        19.96        65.49        32.15        53.59        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       11.51        59.18        39.78        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
        4.73        33.37        40.14        58.45        15.68        56.35 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       29.95        27.12        24.30        46.92        45.11         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT 
       14.53        27.25        47.47        41.52        26.07        15.85 
TCGA-VS-A9UU TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       14.53        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR 
        4.34        16.24        15.42        26.01        29.26        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.36              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           154.32            210.67 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           26.745            22.800 
[1] "0.4 - 154.3 (26.7)" "0.0 - 210.7 (22.8)"
[1] "hr=" "1.6"
D55V2, continuous
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED    15   9   1   1
  7Q LOSS WILD-TYPE 120  61  20   7
D55V3, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              15               120
  T2               9                61
  T3               1                20
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    13   8
  7Q LOSS WILD-TYPE 116  48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     13    8
  7Q LOSS WILD-TYPE  116   48
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0              13               116
  1               8                48
[1] 2 2
[1] FALSE
D55V5, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    9  0
  7Q LOSS WILD-TYPE 99 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      9    0
  7Q LOSS WILD-TYPE   99   10
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               9                99
  1               0                10
[1] 2 2
[1] FALSE
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     6  13
  7Q LOSS WILD-TYPE  49 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      6   13
  7Q LOSS WILD-TYPE   49  110
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                6                49
  YES              13               110
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED               0                               29
  7Q LOSS WILD-TYPE             6                              213
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7Q LOSS MUTATED                                               1
  7Q LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7Q LOSS MUTATED                                     5
  7Q LOSS WILD-TYPE                                  16
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7Q LOSS MUTATED                                           0
  7Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7Q LOSS MUTATED                                              2
  7Q LOSS WILD-TYPE                                           15
D55V7, multiclass
                                               clus
vv                                              7Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           29
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              7Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            213
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, continuous
D55V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  1     4
  7Q LOSS WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED                           5
  7Q LOSS WILD-TYPE                        23
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           0    25
  7Q LOSS WILD-TYPE                                         2   177
D55V10, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                               5                23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  25               177
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  28
  7Q LOSS WILD-TYPE  22 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   28
  7Q LOSS WILD-TYPE   22  134
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                22
  NOT HISPANIC OR LATINO              28               134
[1] 2 2
[1] FALSE
D55V12, continuous
D55V13, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    21  13
  7Q LOSS WILD-TYPE 162  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     21   13
  7Q LOSS WILD-TYPE  162   61
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  TUMOR FREE              21               162
  WITH TUMOR              13                61
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  7Q LOSS MUTATED     1  13  20   0   3
  7Q LOSS WILD-TYPE  17 116  95   1  21
D55V14, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  G1               1                17
  G2              13               116
  G3              20                95
  G4               0                 1
  GX               3                21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V15, continuous
D55V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7Q LOSS MUTATED                                             2
  7Q LOSS WILD-TYPE                                          36
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  7Q LOSS MUTATED                                        1
  7Q LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  7Q LOSS MUTATED                                                 0
  7Q LOSS WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7Q LOSS MUTATED                8                  19
  7Q LOSS WILD-TYPE             54                 124
D55V17, multiclass
                                                 clus
vv                                                7Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                8
  LIFELONG NON-SMOKER                                          19
                                                 clus
vv                                                7Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    36
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 54
  LIFELONG NON-SMOKER                                           124
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V18, continuous
D55V19, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    9  2
  7Q LOSS WILD-TYPE 16  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      9    2
  7Q LOSS WILD-TYPE   16    1
                         clus
vv                        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  9                16
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
D55V20, continuous
D55V21, continuous
D55V22, continuous
D55V23, continuous
D55V24, continuous
D55V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  7Q LOSS MUTATED                                     0
  7Q LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  7Q LOSS MUTATED                                     2                       2
  7Q LOSS WILD-TYPE                                   5                      34
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7Q LOSS MUTATED                         0                       1
  7Q LOSS WILD-TYPE                       1                       7
D55V26, multiclass
                                     clus
vv                                    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 5
  OTHER LOCATION, SPECIFY                           2                34
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  7Q LOSS MUTATED                                               0
  7Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  7Q LOSS MUTATED                                                4
  7Q LOSS WILD-TYPE                                             21
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7Q LOSS MUTATED                                                                                  10
  7Q LOSS WILD-TYPE                                                                                72
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7Q LOSS MUTATED                                                                                             16
  7Q LOSS WILD-TYPE                                                                                          105
D55V27, multiclass
                                                                                              clus
vv                                                                                             7Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              16
                                                                                              clus
vv                                                                                             7Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           72
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               105
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V28, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    8 13
  7Q LOSS WILD-TYPE 63 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      8   13
  7Q LOSS WILD-TYPE   63   61
         clus
vv        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ABSENT                8                63
  PRESENT              13                61
[1] 2 2
[1] FALSE
D55V29, continuous
D55V30, continuous
D55V31, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     9  14
  7Q LOSS WILD-TYPE  40 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      9   14
  7Q LOSS WILD-TYPE   40  103
                                          clus
vv                                         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   9                40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              14               103
[1] 2 2
[1] FALSE
D55V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7Q LOSS MUTATED              1           9         11
  7Q LOSS WILD-TYPE           14          45         74
D55V33, multiclass
              clus
vv             7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CURRENT USER               1                14
  FORMER USER                9                45
  NEVER USED                11                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V34, continuous
D55V35, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED   14  1
  7Q LOSS WILD-TYPE 78 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     14    1
  7Q LOSS WILD-TYPE   78   17
         clus
vv        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ABSENT               14                78
  PRESENT               1                17
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  7Q LOSS MUTATED             1        16     1
  7Q LOSS WILD-TYPE           4        84     1
D55V36, multiclass
             clus
vv            7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                16                84
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V37, continuous
D55V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  7Q LOSS MUTATED         0        0         0         0        2        11
  7Q LOSS WILD-TYPE       5        1         1         1       32        66
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  7Q LOSS MUTATED           5        1         2          1          1
  7Q LOSS WILD-TYPE        32        3         6          4          6
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  7Q LOSS MUTATED           7         0          0          4         1
  7Q LOSS WILD-TYPE        37         1          3         38         6
                   vv
clus                STAGE IVB
  7Q LOSS MUTATED           2
  7Q LOSS WILD-TYPE        10
D55V39, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 2                32
  STAGE IB1               11                66
  STAGE IB2                5                32
  STAGE II                 1                 3
  STAGE IIA                2                 6
  STAGE IIA1               1                 4
  STAGE IIA2               1                 6
  STAGE IIB                7                37
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               4                38
  STAGE IVA                1                 6
  STAGE IVB                2                10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    52  26
  8P LOSS WILD-TYPE 159  41
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               78               200 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               26                41 
$`8P LOSS MUTATED`
TCGA-C5-A1BE TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       68.84        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY 
        2.43        20.91        40.93        73.18        73.45        78.35 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XK 
       94.95        13.61         2.73        50.99        45.83        99.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WI 
       14.73         1.12        95.11        36.76        95.67         8.28 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 
       40.87        30.90        31.73        26.01         0.30        14.89 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2RK TCGA-EK-A3GJ 
       12.59        60.72         1.51        19.27         0.43         0.10 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        0.76         0.03        15.22         8.32         1.22        23.84 
TCGA-FU-A3NI TCGA-FU-A3WB TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LH 
       20.98        16.14        17.75        21.67       137.16        78.71 
TCGA-IR-A3LK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A7HU TCGA-MA-AA3Y TCGA-MA-AA42 
       29.85        15.58         8.28        13.35        17.82         8.52 
TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
        2.96         9.04         9.34        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-VS-A8EC TCGA-VS-A8EL TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QH 
       11.67        46.52        65.49        36.13        59.18        39.78 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UQ 
        4.73        33.37        24.30        45.11        14.53        41.52 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-VS-AA62 TCGA-ZJ-A8QQ 
        3.42        18.25        18.84         4.34        15.42        67.59 

$`8P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
        5.46        19.86        67.46        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
        0.46         3.58        44.22        83.05       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A8XI TCGA-C5-A8XJ 
       17.19       155.77       131.11         9.34         8.35       146.86 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-DG-A2KK TCGA-DG-A2KL 
       23.51        27.52        20.81        20.91        82.06        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       63.98        87.75        58.88        55.63        69.96        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS 
       16.83        16.18        17.52        39.55        37.35        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.82         7.46        26.79        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H1 TCGA-EK-A2IP 
       27.22        24.00        13.48         0.36        26.27         6.64 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        0.39         0.43         0.59         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK 
       40.96         4.31         0.10        47.77         0.53         0.49 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A2QG 
       20.35         7.92        14.70        19.79        15.55        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ 
       16.11        31.36        36.26        26.14         1.48        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC 
       14.01        35.44        10.55         1.12        25.41        16.57 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC 
       20.78        14.93         9.44       147.39        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       96.95        81.96        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       21.44        20.48        28.37        18.15        21.11       209.59 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
       44.61        20.91        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 
        0.82        22.52        19.56        19.56         8.35        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       28.08        34.62        19.96        54.81        35.05        20.84 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
       17.23        15.58        16.41        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       14.07        15.88        18.64        93.99        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 
       10.03        45.57        32.42        23.97        19.96        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A950 
       53.59        11.51        31.27        40.87        16.64        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       58.45        15.68        56.35        55.50        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       50.47        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR 
       46.92         1.71        27.25        47.87        47.47        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       15.85        14.53        67.20         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       16.24        26.01        29.26        19.13         0.69         1.41 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           137.16            210.67 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           20.945            23.985 
[1] "0.0 - 137.2 (20.9)" "0.1 - 210.7 (24.0)"
[1] "hr=" "1.8"
D56V2, continuous
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED   37 19  4  2
  8P LOSS WILD-TYPE 98 51 17  6
D56V3, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              37                98
  T2              19                51
  T3               4                17
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   36 13
  8P LOSS WILD-TYPE 93 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     36   13
  8P LOSS WILD-TYPE   93   43
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              36                93
  1              13                43
[1] 2 2
[1] FALSE
D56V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   31  0
  8P LOSS WILD-TYPE 77 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     31    0
  8P LOSS WILD-TYPE   77   10
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              31                77
  1               0                10
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   12 34
  8P LOSS WILD-TYPE 43 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     12   34
  8P LOSS WILD-TYPE   43   89
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               12                43
  YES              34                89
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED               2                               68
  8P LOSS WILD-TYPE             4                              174
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8P LOSS MUTATED                                               1
  8P LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8P LOSS MUTATED                                     4
  8P LOSS WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8P LOSS MUTATED                                           2
  8P LOSS WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8P LOSS MUTATED                                              5
  8P LOSS WILD-TYPE                                           12
D56V7, multiclass
                                               clus
vv                                              8P LOSS MUTATED
  ADENOSQUAMOUS                                               2
  CERVICAL SQUAMOUS CELL CARCINOMA                           68
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                5
                                               clus
vv                                              8P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 4
  CERVICAL SQUAMOUS CELL CARCINOMA                            174
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, continuous
D56V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  3     2
  8P LOSS WILD-TYPE                                5    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED                          10
  8P LOSS WILD-TYPE                        18
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           1    58
  8P LOSS WILD-TYPE                                         1   144
D56V10, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 5
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                              10                18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 1
  WHITE                                                  58               144
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     6  42
  8P LOSS WILD-TYPE  17 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      6   42
  8P LOSS WILD-TYPE   17  120
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                17
  NOT HISPANIC OR LATINO              42               120
[1] 2 2
[1] FALSE
D56V12, continuous
D56V13, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    46  27
  8P LOSS WILD-TYPE 137  47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     46   27
  8P LOSS WILD-TYPE  137   47
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  TUMOR FREE              46               137
  WITH TUMOR              27                47
[1] 2 2
[1] FALSE
                   vv
clus                G1 G2 G3 G4 GX
  8P LOSS MUTATED    3 31 36  1  9
  8P LOSS WILD-TYPE 15 98 79  0 15
D56V14, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  G1               3                15
  G2              31                98
  G3              36                79
  G4               1                 0
  GX               9                15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, continuous
D56V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8P LOSS MUTATED                                            14
  8P LOSS WILD-TYPE                                          24
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  8P LOSS MUTATED                                        1
  8P LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  8P LOSS MUTATED                                                 0
  8P LOSS WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8P LOSS MUTATED               15                  36
  8P LOSS WILD-TYPE             47                 107
D56V17, multiclass
                                                 clus
vv                                                8P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               15
  LIFELONG NON-SMOKER                                          36
                                                 clus
vv                                                8P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    24
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 47
  LIFELONG NON-SMOKER                                           107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V18, continuous
D56V19, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    9  2
  8P LOSS WILD-TYPE 16  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      9    2
  8P LOSS WILD-TYPE   16    1
                         clus
vv                        8P LOSS MUTATED 8P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  9                16
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
D56V20, continuous
D56V21, continuous
D56V22, continuous
D56V23, continuous
D56V24, continuous
D56V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  8P LOSS MUTATED                                     1
  8P LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  8P LOSS MUTATED                                     1                      13
  8P LOSS WILD-TYPE                                   6                      23
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8P LOSS MUTATED                         0                       3
  8P LOSS WILD-TYPE                       1                       5
D56V26, multiclass
                                     clus
vv                                    8P LOSS MUTATED 8P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 6
  OTHER LOCATION, SPECIFY                          13                23
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           3                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  8P LOSS MUTATED                                               1
  8P LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  8P LOSS MUTATED                                                5
  8P LOSS WILD-TYPE                                             20
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8P LOSS MUTATED                                                                                  25
  8P LOSS WILD-TYPE                                                                                57
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8P LOSS MUTATED                                                                                             34
  8P LOSS WILD-TYPE                                                                                           87
D56V27, multiclass
                                                                                              clus
vv                                                                                             8P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              34
                                                                                              clus
vv                                                                                             8P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              20
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V28, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   22 14
  8P LOSS WILD-TYPE 49 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     22   14
  8P LOSS WILD-TYPE   49   60
         clus
vv        8P LOSS MUTATED 8P LOSS WILD-TYPE
  ABSENT               22                49
  PRESENT              14                60
[1] 2 2
[1] FALSE
D56V29, continuous
D56V30, continuous
D56V31, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   16 30
  8P LOSS WILD-TYPE 33 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     16   30
  8P LOSS WILD-TYPE   33   87
                                          clus
vv                                         8P LOSS MUTATED 8P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  16                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              30                87
[1] 2 2
[1] FALSE
D56V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8P LOSS MUTATED              5          14         22
  8P LOSS WILD-TYPE           10          40         63
D56V33, multiclass
              clus
vv             8P LOSS MUTATED 8P LOSS WILD-TYPE
  CURRENT USER               5                10
  FORMER USER               14                40
  NEVER USED                22                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V34, continuous
D56V35, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   27  4
  8P LOSS WILD-TYPE 65 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     27    4
  8P LOSS WILD-TYPE   65   14
         clus
vv        8P LOSS MUTATED 8P LOSS WILD-TYPE
  ABSENT               27                65
  PRESENT               4                14
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  8P LOSS MUTATED             2        30     1
  8P LOSS WILD-TYPE           3        70     1
D56V36, multiclass
             clus
vv            8P LOSS MUTATED 8P LOSS WILD-TYPE
  CARBOPLATIN               2                 3
  CISPLATIN                30                70
  OTHER                     1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V37, continuous
D56V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  8P LOSS MUTATED         2        0         0         1       11        20
  8P LOSS WILD-TYPE       3        1         1         0       23        57
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  8P LOSS MUTATED           7        2         1          4          2
  8P LOSS WILD-TYPE        30        2         7          1          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  8P LOSS MUTATED          15         0          1         10         2
  8P LOSS WILD-TYPE        29         1          2         32         5
                   vv
clus                STAGE IVB
  8P LOSS MUTATED           2
  8P LOSS WILD-TYPE        10
D56V39, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                11                23
  STAGE IB1               20                57
  STAGE IB2                7                30
  STAGE II                 2                 2
  STAGE IIA                1                 7
  STAGE IIA1               4                 1
  STAGE IIA2               2                 5
  STAGE IIB               15                29
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB              10                32
  STAGE IVA                2                 5
  STAGE IVB                2                10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    17   6
  8Q LOSS WILD-TYPE 194  61
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               23               255 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                6                61 
$`8Q LOSS MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT 
       31.40        35.01        57.73        20.91        40.93        73.18 
TCGA-C5-A7X8 TCGA-DG-A2KH TCGA-DS-A0VN TCGA-EA-A439 TCGA-EA-A43B TCGA-EK-A3GJ 
        2.73         1.12        95.67        31.73        26.01         0.10 
TCGA-EK-A3GM TCGA-EX-A3L1 TCGA-LP-A7HU TCGA-PN-A8MA TCGA-UC-A7PD TCGA-VS-A8EL 
        0.76        15.22        13.35         2.96        11.67        65.49 
TCGA-VS-A8QA TCGA-VS-A9UD TCGA-VS-A9UL TCGA-VS-A9UQ TCGA-VS-A9V0 
       36.13        24.30        14.53        41.52        18.84 

$`8Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
       82.85         5.46        19.86        67.46        46.32        30.21 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP 
       53.16        38.99        35.61         0.46         2.43         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19       155.77       131.11        94.95         9.34        13.61 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
       50.99        45.83         8.35       146.86        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KJ TCGA-DG-A2KK 
       27.52        20.81        20.91        14.73        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       69.96        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S 
       13.05        25.02        36.89        26.40        24.56         0.30 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       27.25        27.22        24.00        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
       60.72        26.27         6.64         1.51        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.43         0.59         0.36         1.45         0.13        40.96 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK 
        4.31         0.10         0.43        47.77         0.53         0.49 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03        20.35         7.92        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       15.55         1.22        23.84        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26        20.98        26.14         1.48        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       14.01        35.44        10.55         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       16.57        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       129.37        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        28.37         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
      209.59        44.61        20.91        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.30         0.82        22.52        19.56        17.82        19.56 
TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        8.35         8.52        11.38        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       54.81        35.05        20.84        17.23        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        9.34        18.64        22.62        19.59        14.60        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF 
       23.97        19.96        32.15        53.59        11.51        59.18 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78        31.27        40.87        16.64         4.73        33.37 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       40.14        58.45        15.68        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       51.32        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO 
       27.12        46.92        45.11         1.71        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       47.47        26.07        15.85        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       67.20         5.16        18.25        17.75         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.10              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            95.67            210.67 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            24.30             22.98 
[1] "0.1 - 95.7 (24.3)"  "0.0 - 210.7 (23.0)"
[1] "hr=" "1.3"
D57V2, continuous
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED    10   6   3   0
  8Q LOSS WILD-TYPE 125  64  18   8
D57V3, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              10               125
  T2               6                64
  T3               3                18
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    13   2
  8Q LOSS WILD-TYPE 116  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     13    2
  8Q LOSS WILD-TYPE  116   54
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              13               116
  1               2                54
[1] 2 2
[1] FALSE
D57V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED   13  0
  8Q LOSS WILD-TYPE 95 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     13    0
  8Q LOSS WILD-TYPE   95   10
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              13                95
  1               0                10
[1] 2 2
[1] FALSE
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  11
  8Q LOSS WILD-TYPE  55 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   11
  8Q LOSS WILD-TYPE   55  112
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                55
  YES              11               112
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED               1                               16
  8Q LOSS WILD-TYPE             5                              226
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8Q LOSS MUTATED                                               0
  8Q LOSS WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8Q LOSS MUTATED                                     4
  8Q LOSS WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8Q LOSS MUTATED                                           0
  8Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8Q LOSS MUTATED                                              3
  8Q LOSS WILD-TYPE                                           14
D57V7, multiclass
                                               clus
vv                                              8Q LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           16
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                3
                                               clus
vv                                              8Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            226
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, continuous
D57V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  1     2
  8Q LOSS WILD-TYPE                                7    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED                           2
  8Q LOSS WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           1    14
  8Q LOSS WILD-TYPE                                         1   188
D57V10, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               2                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 1
  WHITE                                                  14               188
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  12
  8Q LOSS WILD-TYPE  22 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   12
  8Q LOSS WILD-TYPE   22  150
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                22
  NOT HISPANIC OR LATINO              12               150
[1] 2 2
[1] FALSE
D57V12, continuous
D57V13, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    13   8
  8Q LOSS WILD-TYPE 170  66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     13    8
  8Q LOSS WILD-TYPE  170   66
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  TUMOR FREE              13               170
  WITH TUMOR               8                66
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  8Q LOSS MUTATED     1   8  13   0   2
  8Q LOSS WILD-TYPE  17 121 102   1  22
D57V14, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  G1               1                17
  G2               8               121
  G3              13               102
  G4               0                 1
  GX               2                22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V15, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                41 
       TCGA-2W-A8YY        TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C5-A1BQ        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A2M2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-C5-A8XH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C5-A907        TCGA-DG-A2KK        TCGA-DS-A3LQ        TCGA-EK-A2RA 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EX-A69M        TCGA-FU-A2QG        TCGA-FU-A3TX        TCGA-FU-A3WB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-HM-A4S6        TCGA-IR-A3L7        TCGA-IR-A3LB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-JX-A3Q0        TCGA-MA-AA43        TCGA-MU-A5YI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-Q1-A73S        TCGA-RA-A741 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-VS-A8QF        TCGA-VS-A94Z        TCGA-VS-A9V4        TCGA-WL-A834 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ZJ-A8QR        TCGA-ZJ-AAX4        TCGA-ZJ-AAXA        TCGA-ZJ-AAXT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ZJ-AB0I 
"8Q LOSS WILD-TYPE" 
D57V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8Q LOSS MUTATED                                             3
  8Q LOSS WILD-TYPE                                          35
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  8Q LOSS MUTATED                                        0
  8Q LOSS WILD-TYPE                                      9
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  8Q LOSS MUTATED                                                 0
  8Q LOSS WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8Q LOSS MUTATED                5                  13
  8Q LOSS WILD-TYPE             57                 130
D57V17, multiclass
                                                 clus
vv                                                8Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                5
  LIFELONG NON-SMOKER                                          13
                                                 clus
vv                                                8Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    35
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 57
  LIFELONG NON-SMOKER                                           130
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V18, continuous
D57V19, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    5  0
  8Q LOSS WILD-TYPE 20  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    0
  8Q LOSS WILD-TYPE   20    3
                         clus
vv                        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  5                20
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D57V20, continuous
D57V21, continuous
D57V22, continuous
D57V23, continuous
D57V24, continuous
D57V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  8Q LOSS MUTATED                                     0
  8Q LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  8Q LOSS MUTATED                                     0                       6
  8Q LOSS WILD-TYPE                                   7                      30
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8Q LOSS MUTATED                         0                       1
  8Q LOSS WILD-TYPE                       1                       7
D57V26, multiclass
                                     clus
vv                                    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 7
  OTHER LOCATION, SPECIFY                           6                30
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  8Q LOSS MUTATED                                               0
  8Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  8Q LOSS MUTATED                                                2
  8Q LOSS WILD-TYPE                                             23
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8Q LOSS MUTATED                                                                                   6
  8Q LOSS WILD-TYPE                                                                                76
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8Q LOSS MUTATED                                                                                             13
  8Q LOSS WILD-TYPE                                                                                          108
D57V27, multiclass
                                                                                              clus
vv                                                                                             8Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              13
                                                                                              clus
vv                                                                                             8Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           76
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V28, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    8  5
  8Q LOSS WILD-TYPE 63 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      8    5
  8Q LOSS WILD-TYPE   63   69
         clus
vv        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ABSENT                8                63
  PRESENT               5                69
[1] 2 2
[1] FALSE
D57V29, continuous
D57V30, continuous
D57V31, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     7   3
  8Q LOSS WILD-TYPE  42 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7    3
  8Q LOSS WILD-TYPE   42  114
                                          clus
vv                                         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   7                42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               3               114
[1] 2 2
[1] FALSE
D57V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8Q LOSS MUTATED              3           8          5
  8Q LOSS WILD-TYPE           12          46         80
D57V33, multiclass
              clus
vv             8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CURRENT USER               3                12
  FORMER USER                8                46
  NEVER USED                 5                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V34, continuous
D57V35, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    9  1
  8Q LOSS WILD-TYPE 83 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9    1
  8Q LOSS WILD-TYPE   83   17
         clus
vv        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ABSENT                9                83
  PRESENT               1                17
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  8Q LOSS MUTATED             0         9     0
  8Q LOSS WILD-TYPE           5        91     2
D57V36, multiclass
             clus
vv            8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CARBOPLATIN               0                 5
  CISPLATIN                 9                91
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V37, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                15 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1MP        TCGA-EK-A2RO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852        TCGA-JX-A3Q8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42        TCGA-MU-A51Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D57V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  8Q LOSS MUTATED         0        0         0         0        6         7
  8Q LOSS WILD-TYPE       5        1         1         1       28        70
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  8Q LOSS MUTATED           1        1         1          2          0
  8Q LOSS WILD-TYPE        36        3         7          3          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  8Q LOSS MUTATED           3         0          1          2         0
  8Q LOSS WILD-TYPE        41         1          2         40         7
                   vv
clus                STAGE IVB
  8Q LOSS MUTATED           0
  8Q LOSS WILD-TYPE        12
D57V39, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                0                 1
  STAGE IA2                0                 1
  STAGE IB                 6                28
  STAGE IB1                7                70
  STAGE IB2                1                36
  STAGE II                 1                 3
  STAGE IIA                1                 7
  STAGE IIA1               2                 3
  STAGE IIA2               0                 7
  STAGE IIB                3                41
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               2                40
  STAGE IVA                0                 7
  STAGE IVB                0                12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    37  14
  9P LOSS WILD-TYPE 174  53
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               51               227 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               14                53 
$`9P LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BJ TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI 
       23.67       144.16        31.40        35.01        57.73        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 
        0.46        40.93       154.32       131.11         9.34        13.61 
TCGA-C5-A8YQ TCGA-DG-A2KJ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 
       23.51        95.11        39.55        40.87        30.90        24.56 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PL 
       26.01         0.30         0.36        12.59         1.51         0.43 
TCGA-EK-A2PM TCGA-EX-A69M TCGA-FU-A3YQ TCGA-HM-A3JJ TCGA-LP-A4AW TCGA-MA-AA3X 
        0.59         8.32        28.31        21.67         0.89        19.56 
TCGA-MA-AA43 TCGA-MU-A5YI TCGA-MY-A5BD TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       11.38        34.62        54.81        15.58        16.41         9.04 
TCGA-Q1-A73S TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 
       22.62        10.03        46.52        23.97        19.96        53.59 
TCGA-VS-A8QF TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9UI TCGA-VS-A9UR TCGA-VS-A9UT 
       59.18        51.32        43.40        45.11        26.07        15.85 
TCGA-VS-A9V0 TCGA-VS-A9V3 TCGA-ZJ-AAX4 
       18.84        17.75         0.69 

$`9P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       18.74        36.56       177.04       173.29        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH 
       19.86        67.46        46.32        30.21        53.16        38.99 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        2.43        20.91         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42       210.67       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        2.73        50.99        45.83         8.35       146.86        99.91 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       27.52        20.81        20.91        14.73         1.12        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       69.96        95.67        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        8.28        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       36.89        26.40        31.73        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK 
       13.48        60.72        26.27         6.64        19.27         0.39 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.36         1.45         0.13        40.96         4.31         0.10 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM 
        0.43        47.77         0.53         0.10         0.49         0.76 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92        15.22        14.70        19.79 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       15.55         1.22        23.84        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A40J 
       36.26        20.98        26.14         1.48        16.14        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       35.44        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       20.91        11.28        12.49         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y 
       22.52        17.82        19.56         8.35         8.52        28.08 
TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 
       19.96        35.05        20.84        17.23         2.96        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59        14.60        11.67        93.99        12.16        69.50 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC 
       45.57        32.42        65.49        32.15        36.13        11.51 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z 
       39.78        31.27        40.87        16.64         4.73        33.37 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       40.14        58.45        15.68        56.35        55.50        50.14 
TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       50.47        48.39        28.50        29.95        27.12        24.30 
TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP 
       46.92         1.71        14.53        27.25        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 
       41.52        14.53         3.42        18.25        67.20         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       18.25         4.34        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.30              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           154.32            210.67 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            23.67             22.52 
[1] "0.3 - 154.3 (23.7)" "0.0 - 210.7 (22.5)"
[1] "hr=" "1.2"
D58V2, continuous
                   vv
clus                 T1  T2  T3  T4
  9P LOSS MUTATED    20   9   6   2
  9P LOSS WILD-TYPE 115  61  15   6
D58V3, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              20               115
  T2               9                61
  T3               6                15
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    17   7
  9P LOSS WILD-TYPE 112  49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     17    7
  9P LOSS WILD-TYPE  112   49
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              17               112
  1               7                49
[1] 2 2
[1] FALSE
D58V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   19  3
  9P LOSS WILD-TYPE 89  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     19    3
  9P LOSS WILD-TYPE   89    7
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              19                89
  1               3                 7
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    10  22
  9P LOSS WILD-TYPE  45 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     10   22
  9P LOSS WILD-TYPE   45  101
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               10                45
  YES              22               101
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED               1                               46
  9P LOSS WILD-TYPE             5                              196
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9P LOSS MUTATED                                               0
  9P LOSS WILD-TYPE                                             6
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9P LOSS MUTATED                                     3
  9P LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9P LOSS MUTATED                                           0
  9P LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9P LOSS MUTATED                                              4
  9P LOSS WILD-TYPE                                           13
D58V7, multiclass
                                               clus
vv                                              9P LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           46
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                4
                                               clus
vv                                              9P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            196
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, continuous
D58V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     3
  9P LOSS WILD-TYPE                                8    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED                           6
  9P LOSS WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           0    42
  9P LOSS WILD-TYPE                                         2   160
D58V10, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               6                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  42               160
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2  31
  9P LOSS WILD-TYPE  21 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2   31
  9P LOSS WILD-TYPE   21  131
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                21
  NOT HISPANIC OR LATINO              31               131
[1] 2 2
[1] FALSE
D58V12, continuous
D58V13, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    33  18
  9P LOSS WILD-TYPE 150  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     33   18
  9P LOSS WILD-TYPE  150   56
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  TUMOR FREE              33               150
  WITH TUMOR              18                56
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  9P LOSS MUTATED     4  24  19   0   6
  9P LOSS WILD-TYPE  14 105  96   1  18
D58V14, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  G1               4                14
  G2              24               105
  G3              19                96
  G4               0                 1
  GX               6                18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, continuous
D58V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9P LOSS MUTATED                                             8
  9P LOSS WILD-TYPE                                          30
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  9P LOSS MUTATED                                        1
  9P LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  9P LOSS MUTATED                                                 0
  9P LOSS WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9P LOSS MUTATED                6                  28
  9P LOSS WILD-TYPE             56                 115
D58V17, multiclass
                                                 clus
vv                                                9P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                6
  LIFELONG NON-SMOKER                                          28
                                                 clus
vv                                                9P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 56
  LIFELONG NON-SMOKER                                           115
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V18, continuous
D58V19, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    6  0
  9P LOSS WILD-TYPE 19  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6    0
  9P LOSS WILD-TYPE   19    3
                         clus
vv                        9P LOSS MUTATED 9P LOSS WILD-TYPE
  COMPLETED AS PLANNED                  6                19
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D58V20, continuous
D58V21, continuous
D58V22, continuous
D58V23, continuous
D58V24, continuous
D58V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  9P LOSS MUTATED                                     0
  9P LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  9P LOSS MUTATED                                     1                       4
  9P LOSS WILD-TYPE                                   6                      32
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9P LOSS MUTATED                         0                       1
  9P LOSS WILD-TYPE                       1                       7
D58V26, multiclass
                                     clus
vv                                    9P LOSS MUTATED 9P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 6
  OTHER LOCATION, SPECIFY                           4                32
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  9P LOSS MUTATED                                               0
  9P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  9P LOSS MUTATED                                                4
  9P LOSS WILD-TYPE                                             21
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9P LOSS MUTATED                                                                                  21
  9P LOSS WILD-TYPE                                                                                61
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9P LOSS MUTATED                                                                                             17
  9P LOSS WILD-TYPE                                                                                          104
D58V27, multiclass
                                                                                              clus
vv                                                                                             9P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              17
                                                                                              clus
vv                                                                                             9P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           61
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V28, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    9 11
  9P LOSS WILD-TYPE 62 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      9   11
  9P LOSS WILD-TYPE   62   63
         clus
vv        9P LOSS MUTATED 9P LOSS WILD-TYPE
  ABSENT                9                62
  PRESENT              11                63
[1] 2 2
[1] FALSE
D58V29, continuous
D58V30, continuous
D58V31, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    7 23
  9P LOSS WILD-TYPE 42 94
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7   23
  9P LOSS WILD-TYPE   42   94
                                          clus
vv                                         9P LOSS MUTATED 9P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   7                42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              23                94
[1] 2 2
[1] FALSE
D58V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9P LOSS MUTATED              1          12         18
  9P LOSS WILD-TYPE           14          42         67
D58V33, multiclass
              clus
vv             9P LOSS MUTATED 9P LOSS WILD-TYPE
  CURRENT USER               1                14
  FORMER USER               12                42
  NEVER USED                18                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V34, continuous
D58V35, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   13  3
  9P LOSS WILD-TYPE 79 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     13    3
  9P LOSS WILD-TYPE   79   15
         clus
vv        9P LOSS MUTATED 9P LOSS WILD-TYPE
  ABSENT               13                79
  PRESENT               3                15
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  9P LOSS MUTATED             1        19     0
  9P LOSS WILD-TYPE           4        81     2
D58V36, multiclass
             clus
vv            9P LOSS MUTATED 9P LOSS WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                19                81
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V37, continuous
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MP 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK        TCGA-JW-A852 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-JX-A3Q8        TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
D58V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  9P LOSS MUTATED         1        1         1         0        5        14
  9P LOSS WILD-TYPE       4        0         0         1       29        63
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  9P LOSS MUTATED           2        2         2          0          0
  9P LOSS WILD-TYPE        35        2         6          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  9P LOSS MUTATED          10         0          0         11         0
  9P LOSS WILD-TYPE        34         1          3         31         7
                   vv
clus                STAGE IVB
  9P LOSS MUTATED           3
  9P LOSS WILD-TYPE         9
D58V39, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 1                 0
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                 5                29
  STAGE IB1               14                63
  STAGE IB2                2                35
  STAGE II                 2                 2
  STAGE IIA                2                 6
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB               10                34
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB              11                31
  STAGE IVA                0                 7
  STAGE IVB                3                 9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    33  14
  9Q LOSS WILD-TYPE 178  53
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               47               231 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               14                53 
$`9Q LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ 
       23.67        31.40        35.01        57.73        35.61         0.46 
TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8YQ 
      154.32       131.11         9.34        13.61         2.73        23.51 
TCGA-DG-A2KJ TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A97N 
       95.11        39.55        40.87        24.56        26.01         0.36 
TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A3GM TCGA-EX-A69M TCGA-HM-A3JJ 
       12.59         1.51         0.43         0.76         8.32        21.67 
TCGA-IR-A3LF TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-MA-AA3X TCGA-MA-AA43 TCGA-MU-A5YI 
       96.95        21.11        44.61        19.56        11.38        34.62 
TCGA-MY-A5BD TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-VS-A8EB TCGA-VS-A8EC 
       54.81         2.96        15.58        16.41        10.03        46.52 
TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A950 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9UI 
       19.96        59.18        40.14        51.32        43.40        45.11 
TCGA-VS-A9UL TCGA-VS-A9UT TCGA-VS-A9V0 TCGA-VS-A9V3 TCGA-ZJ-AAX4 
       14.53        15.85        18.84        17.75         0.69 

$`9Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF 
        5.46        19.86        67.46        46.32        30.21        53.16 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
      155.77        94.95        50.99        45.83         8.35       146.86 
TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       99.91        27.52        20.81        20.91        14.73         1.12 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       55.63        69.96        95.67        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       17.52         8.28        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A44S 
       13.05        25.02        36.89        26.40        31.73         0.30 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 
       27.25        27.22        24.00        13.48        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64        19.27         0.39         0.59         0.36         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL 
        0.13        40.96         4.31         0.10         0.43        47.77 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.53         0.10         0.49         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L 
       15.22        14.70        19.79        15.55         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
        1.12        17.75        25.41        16.57        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH 
        9.44       147.39       137.16        66.81       129.37        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
      209.59        20.91        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
        0.82        13.35        22.52        17.82        19.56         8.35 
TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
        8.52        28.08        19.96        35.05        20.84        17.23 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        9.34        18.64        22.62        19.59        14.60        11.67 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       93.99        12.16        69.50        45.57        32.42        23.97 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH 
       65.49        32.15        53.59        36.13        11.51        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 
       31.27        40.87        16.64         4.73        33.37        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U7 
       15.68        56.35        55.50        50.14        50.47        48.39 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ 
       28.50        29.95        27.12        24.30        46.92         1.71 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU 
       27.25        47.87        47.47        41.52        26.07        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V4 
        3.42        18.25        67.20         5.16        18.25         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.36              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           154.32            210.67 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            21.67             23.84 
[1] "0.4 - 154.3 (21.7)" "0.0 - 210.7 (23.8)"
[1] "hr=" "1.4"
D59V2, continuous
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED    20   9   7   2
  9Q LOSS WILD-TYPE 115  61  14   6
D59V3, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              20               115
  T2               9                61
  T3               7                14
  T4               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    18   6
  9Q LOSS WILD-TYPE 111  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     18    6
  9Q LOSS WILD-TYPE  111   50
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              18               111
  1               6                50
[1] 2 2
[1] FALSE
D59V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   20  3
  9Q LOSS WILD-TYPE 88  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     20    3
  9Q LOSS WILD-TYPE   88    7
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              20                88
  1               3                 7
[1] 2 2
[1] FALSE
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     9  23
  9Q LOSS WILD-TYPE  46 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9   23
  9Q LOSS WILD-TYPE   46  100
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                9                46
  YES              23               100
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED               0                               40
  9Q LOSS WILD-TYPE             6                              202
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9Q LOSS MUTATED                                               2
  9Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9Q LOSS MUTATED                                     5
  9Q LOSS WILD-TYPE                                  16
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9Q LOSS MUTATED                                           0
  9Q LOSS WILD-TYPE                                         3
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9Q LOSS MUTATED                                              4
  9Q LOSS WILD-TYPE                                           13
D59V7, multiclass
                                               clus
vv                                              9Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           40
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                4
                                               clus
vv                                              9Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 6
  CERVICAL SQUAMOUS CELL CARCINOMA                            202
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, continuous
D59V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     2
  9Q LOSS WILD-TYPE                                8    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED                           7
  9Q LOSS WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           0    37
  9Q LOSS WILD-TYPE                                         2   165
D59V10, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               7                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 2
  WHITE                                                  37               165
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     3  27
  9Q LOSS WILD-TYPE  20 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3   27
  9Q LOSS WILD-TYPE   20  135
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                20
  NOT HISPANIC OR LATINO              27               135
[1] 2 2
[1] FALSE
D59V12, continuous
D59V13, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    26  19
  9Q LOSS WILD-TYPE 157  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     26   19
  9Q LOSS WILD-TYPE  157   55
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  TUMOR FREE              26               157
  WITH TUMOR              19                55
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  9Q LOSS MUTATED     2  22  23   0   3
  9Q LOSS WILD-TYPE  16 107  92   1  21
D59V14, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  G1               2                16
  G2              22               107
  G3              23                92
  G4               0                 1
  GX               3                21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V15, continuous
D59V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9Q LOSS MUTATED                                             6
  9Q LOSS WILD-TYPE                                          32
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  9Q LOSS MUTATED                                        1
  9Q LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  9Q LOSS MUTATED                                                 0
  9Q LOSS WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9Q LOSS MUTATED                5                  27
  9Q LOSS WILD-TYPE             57                 116
D59V17, multiclass
                                                 clus
vv                                                9Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                5
  LIFELONG NON-SMOKER                                          27
                                                 clus
vv                                                9Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 57
  LIFELONG NON-SMOKER                                           116
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V18, continuous
D59V19, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    4  0
  9Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4    0
  9Q LOSS WILD-TYPE   21    3
                         clus
vv                        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                  4                21
  TREATMENT NOT COMPLETED               0                 3
[1] 2 2
[1] FALSE
D59V20, continuous
D59V21, continuous
D59V22, continuous
D59V23, continuous
D59V24, continuous
D59V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  9Q LOSS MUTATED                                     0
  9Q LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  9Q LOSS MUTATED                                     1                       5
  9Q LOSS WILD-TYPE                                   6                      31
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9Q LOSS MUTATED                         0                       1
  9Q LOSS WILD-TYPE                       1                       7
D59V26, multiclass
                                     clus
vv                                    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 6
  OTHER LOCATION, SPECIFY                           5                31
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  9Q LOSS MUTATED                                               0
  9Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  9Q LOSS MUTATED                                                3
  9Q LOSS WILD-TYPE                                             22
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9Q LOSS MUTATED                                                                                  20
  9Q LOSS WILD-TYPE                                                                                62
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9Q LOSS MUTATED                                                                                             15
  9Q LOSS WILD-TYPE                                                                                          106
D59V27, multiclass
                                                                                              clus
vv                                                                                             9Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              15
                                                                                              clus
vv                                                                                             9Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           62
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V28, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   10 12
  9Q LOSS WILD-TYPE 61 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     10   12
  9Q LOSS WILD-TYPE   61   62
         clus
vv        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ABSENT               10                61
  PRESENT              12                62
[1] 2 2
[1] FALSE
D59V29, continuous
D59V30, continuous
D59V31, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    5 20
  9Q LOSS WILD-TYPE 44 97
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5   20
  9Q LOSS WILD-TYPE   44   97
                                          clus
vv                                         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                44
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              20                97
[1] 2 2
[1] FALSE
D59V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9Q LOSS MUTATED              1          11         18
  9Q LOSS WILD-TYPE           14          43         67
D59V33, multiclass
              clus
vv             9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CURRENT USER               1                14
  FORMER USER               11                43
  NEVER USED                18                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V34, continuous
D59V35, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   15  2
  9Q LOSS WILD-TYPE 77 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     15    2
  9Q LOSS WILD-TYPE   77   16
         clus
vv        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ABSENT               15                77
  PRESENT               2                16
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  9Q LOSS MUTATED             1        17     0
  9Q LOSS WILD-TYPE           4        83     2
D59V36, multiclass
             clus
vv            9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                17                83
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V37, continuous
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                16 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1ML        TCGA-C5-A1MN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-GH-A9DA        TCGA-HM-A3JK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-MA-AA3W        TCGA-MA-AA3Z        TCGA-MA-AA42 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MU-A8JM        TCGA-MY-A913        TCGA-ZX-AA5X 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
D59V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  9Q LOSS MUTATED         0        0         1         0        5        14
  9Q LOSS WILD-TYPE       5        1         0         1       29        63
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  9Q LOSS MUTATED           3        1         2          0          0
  9Q LOSS WILD-TYPE        34        3         6          5          7
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  9Q LOSS MUTATED           9         0          1         10         0
  9Q LOSS WILD-TYPE        35         1          2         32         7
                   vv
clus                STAGE IVB
  9Q LOSS MUTATED           3
  9Q LOSS WILD-TYPE         9
D59V39, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 0                 1
  STAGE IA1                1                 0
  STAGE IA2                0                 1
  STAGE IB                 5                29
  STAGE IB1               14                63
  STAGE IB2                3                34
  STAGE II                 1                 3
  STAGE IIA                2                 6
  STAGE IIA1               0                 5
  STAGE IIA2               0                 7
  STAGE IIB                9                35
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB              10                32
  STAGE IVA                0                 7
  STAGE IVB                3                 9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    43  18
  10P LOSS WILD-TYPE 168  49
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                61                217 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                18                 49 
$`10P LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1MH 
       23.67        11.44        82.85        19.86        31.40        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LV 
       35.61         0.46        20.91        40.93        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7X8 TCGA-C5-A8YR 
       83.05       210.67        20.35       147.35         2.73        27.52 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF 
       95.11        44.94        13.05        31.73        14.89        27.22 
TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EX-A1H5 
       26.27        19.27         0.59         0.43         0.53        20.35 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A40J TCGA-HM-A3JK TCGA-IR-A3LB TCGA-IR-A3LH 
        1.22        19.04        14.01        20.78        66.81        78.71 
TCGA-JW-A5VK TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MY-A913 
       20.48        44.61        12.49         8.52        11.38        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EL 
        2.96        16.41         9.04        93.99        12.16        65.49 
TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI 
        4.73        40.14        56.35        24.30        46.92        45.11 
TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       47.47        26.07        18.84         4.34        19.13         0.69 
TCGA-ZJ-AAXA 
        1.41 

$`10P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF 
       17.52        17.82        49.48        57.04        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M5 
       36.56       144.16       177.04       173.29         5.46        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MK 
       46.32        30.21        35.01        57.73        53.16         2.43 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
        3.58        44.22        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
       52.01        18.02        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
      134.33        15.48        17.19       155.77       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
        9.34        13.61        50.99        45.83         8.35       146.86 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       99.91        23.51        20.81        20.91        14.73         1.12 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       82.06        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       69.96        95.67        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28        39.55        40.87        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       31.36        25.02        36.89        26.40        24.56        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
        0.30        24.82         7.46        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       27.25        24.00        13.48         0.36        12.59        60.72 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 
        6.64         1.51         0.39         0.43         0.36         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A3GJ 
        0.13        40.96         4.31         0.10        47.77         0.10 
TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.49         0.76         0.03         7.92        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY 
       19.79         8.32        15.55        23.84        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26        20.98        26.14         1.48        16.14        28.31 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       35.44        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC 
       21.67        14.93         9.44       147.39       137.16       129.37 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       96.95        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       24.56        21.44        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 
       21.11       209.59        20.91        11.28         0.89         0.30 
TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z 
        0.82        13.35        22.52        19.56        17.82        19.56 
TCGA-MA-AA41 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        8.35        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       20.84        15.58        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       11.67        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       23.97        19.96        32.15        53.59        36.13        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z 
       59.18        39.78        31.27        40.87        16.64        33.37 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       58.45        15.68        55.50        50.14        51.32        50.47 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ 
       43.40        48.39        28.50        29.95        27.12         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9UU 
       14.53        27.25        47.87        41.52        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
        3.42        18.25        67.20         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXU 
       16.24        15.42        26.01        29.26        67.59         0.16 
TCGA-ZX-AA5X 
        3.91 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.43               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            210.67             209.59 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             20.78              23.84 
[1] "0.4 - 210.7 (20.8)" "0.0 - 209.6 (23.8)"
[1] "hr=" "1.4"
D60V2, continuous
                    vv
clus                  T1  T2  T3  T4
  10P LOSS MUTATED    22  21   6   2
  10P LOSS WILD-TYPE 113  49  15   6
D60V3, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               22                113
  T2               21                 49
  T3                6                 15
  T4                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    21  17
  10P LOSS WILD-TYPE 108  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     21   17
  10P LOSS WILD-TYPE  108   39
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               21                108
  1               17                 39
[1] 2 2
[1] FALSE
D60V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   21  1
  10P LOSS WILD-TYPE 87  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     21    1
  10P LOSS WILD-TYPE   87    9
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               21                 87
  1                1                  9
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    9 28
  10P LOSS WILD-TYPE 46 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      9   28
  10P LOSS WILD-TYPE   46   95
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 9                 46
  YES               28                 95
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED               0                               55
  10P LOSS WILD-TYPE             6                              187
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10P LOSS MUTATED                                               1
  10P LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10P LOSS MUTATED                                     4
  10P LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10P LOSS MUTATED                                           1
  10P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10P LOSS MUTATED                                              5
  10P LOSS WILD-TYPE                                           12
D60V7, multiclass
                                               clus
vv                                              10P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            55
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 5
                                               clus
vv                                              10P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             187
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, continuous
D60V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     4
  10P LOSS WILD-TYPE                                8    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED                          10
  10P LOSS WILD-TYPE                        18
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           1    43
  10P LOSS WILD-TYPE                                         1   159
D60V10, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                               10                 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  1
  WHITE                                                   43                159
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4  36
  10P LOSS WILD-TYPE  19 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4   36
  10P LOSS WILD-TYPE   19  126
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 19
  NOT HISPANIC OR LATINO               36                126
[1] 2 2
[1] FALSE
D60V12, continuous
D60V13, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    35  19
  10P LOSS WILD-TYPE 148  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     35   19
  10P LOSS WILD-TYPE  148   55
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  TUMOR FREE               35                148
  WITH TUMOR               19                 55
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  10P LOSS MUTATED     2  21  35   1   6
  10P LOSS WILD-TYPE  16 108  80   0  18
D60V14, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  G1                2                 16
  G2               21                108
  G3               35                 80
  G4                1                  0
  GX                6                 18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, continuous
D60V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10P LOSS MUTATED                                            12
  10P LOSS WILD-TYPE                                          26
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  10P LOSS MUTATED                                        5
  10P LOSS WILD-TYPE                                      4
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  10P LOSS MUTATED                                                 1
  10P LOSS WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10P LOSS MUTATED               15                  22
  10P LOSS WILD-TYPE             47                 121
D60V17, multiclass
                                                 clus
vv                                                10P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                15
  LIFELONG NON-SMOKER                                           22
                                                 clus
vv                                                10P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  47
  LIFELONG NON-SMOKER                                            121
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V18, continuous
D60V19, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    9  1
  10P LOSS WILD-TYPE 16  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      9    1
  10P LOSS WILD-TYPE   16    2
                         clus
vv                        10P LOSS MUTATED 10P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D60V20, continuous
D60V21, continuous
D60V22, continuous
D60V23, continuous
D60V24, continuous
D60V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  10P LOSS MUTATED                                     0
  10P LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  10P LOSS MUTATED                                     3
  10P LOSS WILD-TYPE                                   4
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  10P LOSS MUTATED                         6                       0
  10P LOSS WILD-TYPE                      30                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10P LOSS MUTATED                         5
  10P LOSS WILD-TYPE                       3
D60V26, multiclass
                                     clus
vv                                    10P LOSS MUTATED 10P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                3                  4
  OTHER LOCATION, SPECIFY                            6                 30
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            5                  3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  10P LOSS MUTATED                                               0
  10P LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  10P LOSS MUTATED                                                6
  10P LOSS WILD-TYPE                                             19
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10P LOSS MUTATED                                                                                  23
  10P LOSS WILD-TYPE                                                                                59
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10P LOSS MUTATED                                                                                             22
  10P LOSS WILD-TYPE                                                                                           99
D60V27, multiclass
                                                                                              clus
vv                                                                                             10P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               22
                                                                                              clus
vv                                                                                             10P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            59
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V28, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    9 20
  10P LOSS WILD-TYPE 62 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      9   20
  10P LOSS WILD-TYPE   62   54
         clus
vv        10P LOSS MUTATED 10P LOSS WILD-TYPE
  ABSENT                 9                 62
  PRESENT               20                 54
[1] 2 2
[1] FALSE
D60V29, continuous
D60V30, continuous
D60V31, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   16 22
  10P LOSS WILD-TYPE 33 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     16   22
  10P LOSS WILD-TYPE   33   95
                                          clus
vv                                         10P LOSS MUTATED 10P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   16                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               22                 95
[1] 2 2
[1] FALSE
D60V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10P LOSS MUTATED              2          11         18
  10P LOSS WILD-TYPE           13          43         67
D60V33, multiclass
              clus
vv             10P LOSS MUTATED 10P LOSS WILD-TYPE
  CURRENT USER                2                 13
  FORMER USER                11                 43
  NEVER USED                 18                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V34, continuous
D60V35, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   16  4
  10P LOSS WILD-TYPE 76 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     16    4
  10P LOSS WILD-TYPE   76   14
         clus
vv        10P LOSS MUTATED 10P LOSS WILD-TYPE
  ABSENT                16                 76
  PRESENT                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  10P LOSS MUTATED             0        26     1
  10P LOSS WILD-TYPE           5        74     1
D60V36, multiclass
             clus
vv            10P LOSS MUTATED 10P LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 26                 74
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V37, continuous
D60V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  10P LOSS MUTATED         2        0         0         1        7        14
  10P LOSS WILD-TYPE       3        1         1         0       27        63
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  10P LOSS MUTATED           6        1         5          2          1
  10P LOSS WILD-TYPE        31        3         3          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  10P LOSS MUTATED          10         0          2         12         2
  10P LOSS WILD-TYPE        34         1          1         30         5
                    vv
clus                 STAGE IVB
  10P LOSS MUTATED           0
  10P LOSS WILD-TYPE        12
D60V39, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  7                 27
  STAGE IB1                14                 63
  STAGE IB2                 6                 31
  STAGE II                  1                  3
  STAGE IIA                 5                  3
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                10                 34
  STAGE III                 0                  1
  STAGE IIIA                2                  1
  STAGE IIIB               12                 30
  STAGE IVA                 2                  5
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    50  19
  10Q LOSS WILD-TYPE 161  48
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                69                209 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                19                 48 
$`10Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M6 
       57.04        23.67        11.44        82.85        19.86        31.40 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A2LT TCGA-C5-A2LV 
       38.99        35.61         0.46        20.91        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7X5 TCGA-C5-A7X8 
       83.05       210.67        20.35       147.35        13.61         2.73 
TCGA-C5-A8YR TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VK TCGA-EA-A3QD TCGA-EA-A439 
       27.52        95.11        44.94        36.76        13.05        31.73 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PI 
       14.89        27.22        13.48        12.59        26.27        19.27 
TCGA-EK-A2PM TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG 
        0.59         0.43         0.53        20.35         1.22        19.04 
TCGA-FU-A3TQ TCGA-FU-A40J TCGA-GH-A9DA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LB 
       26.14        14.01        17.75        21.67        20.78        66.81 
TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-A69B TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-MA-AA42 
       78.71        20.48        28.37        44.61        12.49         8.52 
TCGA-MA-AA43 TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-UC-A7PG 
       11.38        17.23         2.96        16.41         9.04        12.16 
TCGA-UC-A7PI TCGA-VS-A8EL TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A9U5 
       69.50        65.49         4.73        40.14        56.35        50.47 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UP TCGA-VS-A9UR TCGA-VS-A9V0 
       24.30        46.92        45.11        47.47        26.07        18.84 
TCGA-VS-A9V4 TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
        4.34        19.13         0.69 

$`10Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       17.52        17.82        49.48        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M7 
      144.16       177.04       173.29         5.46        67.46        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN 
       30.21        35.01        57.73        53.16         2.43        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
        3.58        44.22        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ 
       52.01        18.02        17.85        20.42       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
      134.33        15.48        17.19       155.77       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        9.34        50.99        45.83         8.35       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK 
       23.51        20.81        20.91        14.73         1.12        82.06 
TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       63.98        87.75        58.88        55.63        69.96        95.67 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
       40.87        37.35        30.90        31.53        31.36        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       36.89        26.40        24.56        26.01         0.30        24.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
        7.46        26.79        25.91        27.29        27.25        24.00 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL 
        0.36        60.72         6.64         1.51         0.39         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.36         1.45         0.13        40.96         4.31         0.10 
TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H6 
       47.77         0.10         0.49         0.76         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23L 
       15.22        14.70        19.79         8.32        15.55        23.84 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB 
       16.11        31.36        36.26        20.98         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC 
       28.31        35.44        10.55         1.12        25.41        16.57 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       147.39       137.16       129.37        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       21.44        15.58         8.28        18.15        21.11       209.59 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       20.91        11.28         0.89         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MU-A51Y 
       22.52        19.56        17.82        19.56         8.35        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
       34.62        19.96        54.81        35.05        20.84        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       10.03        46.52        45.57        32.42        23.97        19.96 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        53.59        36.13        11.51        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 
       31.27        40.87        16.64        33.37        58.45        15.68 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       55.50        50.14        51.32        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       29.95        27.12         1.71        14.53        27.25        47.87 
TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.52        15.85        14.53         3.42        18.25        67.20 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
        5.16        18.25        17.75        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26        67.59         1.41         0.16         3.91 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.43               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            210.67             209.59 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             20.91              23.84 
[1] "0.4 - 210.7 (20.9)" "0.0 - 209.6 (23.8)"
[1] "hr=" "1.3"
D61V2, continuous
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED    29  21   6   2
  10Q LOSS WILD-TYPE 106  49  15   6
D61V3, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               29                106
  T2               21                 49
  T3                6                 15
  T4                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    24  18
  10Q LOSS WILD-TYPE 105  38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     24   18
  10Q LOSS WILD-TYPE  105   38
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               24                105
  1               18                 38
[1] 2 2
[1] FALSE
D61V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   24  1
  10Q LOSS WILD-TYPE 84  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     24    1
  10Q LOSS WILD-TYPE   84    9
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               24                 84
  1                1                  9
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   12 30
  10Q LOSS WILD-TYPE 43 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     12   30
  10Q LOSS WILD-TYPE   43   93
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                12                 43
  YES               30                 93
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED               0                               60
  10Q LOSS WILD-TYPE             6                              182
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10Q LOSS MUTATED                                               2
  10Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10Q LOSS MUTATED                                     5
  10Q LOSS WILD-TYPE                                  16
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10Q LOSS MUTATED                                           2
  10Q LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10Q LOSS MUTATED                                              5
  10Q LOSS WILD-TYPE                                           12
D61V7, multiclass
                                               clus
vv                                              10Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            60
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 5
                                               clus
vv                                              10Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             182
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, continuous
D61V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     5
  10Q LOSS WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED                          13
  10Q LOSS WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           1    48
  10Q LOSS WILD-TYPE                                         1   154
D61V10, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                               13                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  1
  WHITE                                                   48                154
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5  43
  10Q LOSS WILD-TYPE  18 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5   43
  10Q LOSS WILD-TYPE   18  119
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 18
  NOT HISPANIC OR LATINO               43                119
[1] 2 2
[1] FALSE
D61V12, continuous
D61V13, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    41  23
  10Q LOSS WILD-TYPE 142  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     41   23
  10Q LOSS WILD-TYPE  142   51
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  TUMOR FREE               41                142
  WITH TUMOR               23                 51
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  10Q LOSS MUTATED     3  20  43   1   7
  10Q LOSS WILD-TYPE  15 109  72   0  17
D61V14, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  G1                3                 15
  G2               20                109
  G3               43                 72
  G4                1                  0
  GX                7                 17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V15, continuous
D61V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10Q LOSS MUTATED                                            12
  10Q LOSS WILD-TYPE                                          26
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  10Q LOSS MUTATED                                        4
  10Q LOSS WILD-TYPE                                      5
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  10Q LOSS MUTATED                                                 1
  10Q LOSS WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10Q LOSS MUTATED               16                  27
  10Q LOSS WILD-TYPE             46                 116
D61V17, multiclass
                                                 clus
vv                                                10Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                16
  LIFELONG NON-SMOKER                                           27
                                                 clus
vv                                                10Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  46
  LIFELONG NON-SMOKER                                            116
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V18, continuous
D61V19, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    9  1
  10Q LOSS WILD-TYPE 16  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      9    1
  10Q LOSS WILD-TYPE   16    2
                         clus
vv                        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D61V20, continuous
D61V21, continuous
D61V22, continuous
D61V23, continuous
D61V24, continuous
D61V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  10Q LOSS MUTATED                                     0
  10Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  10Q LOSS MUTATED                                     3
  10Q LOSS WILD-TYPE                                   4
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  10Q LOSS MUTATED                         6                       0
  10Q LOSS WILD-TYPE                      30                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10Q LOSS MUTATED                         6
  10Q LOSS WILD-TYPE                       2
D61V26, multiclass
                                     clus
vv                                    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                3                  4
  OTHER LOCATION, SPECIFY                            6                 30
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            6                  2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  10Q LOSS MUTATED                                               0
  10Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  10Q LOSS MUTATED                                                8
  10Q LOSS WILD-TYPE                                             17
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10Q LOSS MUTATED                                                                                  25
  10Q LOSS WILD-TYPE                                                                                57
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10Q LOSS MUTATED                                                                                             24
  10Q LOSS WILD-TYPE                                                                                           97
D61V27, multiclass
                                                                                              clus
vv                                                                                             10Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               24
                                                                                              clus
vv                                                                                             10Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V28, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   12 23
  10Q LOSS WILD-TYPE 59 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     12   23
  10Q LOSS WILD-TYPE   59   51
         clus
vv        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ABSENT                12                 59
  PRESENT               23                 51
[1] 2 2
[1] FALSE
D61V29, continuous
D61V30, continuous
D61V31, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   15 28
  10Q LOSS WILD-TYPE 34 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     15   28
  10Q LOSS WILD-TYPE   34   89
                                          clus
vv                                         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   15                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               28                 89
[1] 2 2
[1] FALSE
D61V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10Q LOSS MUTATED              2          12         20
  10Q LOSS WILD-TYPE           13          42         65
D61V33, multiclass
              clus
vv             10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CURRENT USER                2                 13
  FORMER USER                12                 42
  NEVER USED                 20                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V34, continuous
D61V35, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   19  4
  10Q LOSS WILD-TYPE 73 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     19    4
  10Q LOSS WILD-TYPE   73   14
         clus
vv        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ABSENT                19                 73
  PRESENT                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  10Q LOSS MUTATED             1        28     1
  10Q LOSS WILD-TYPE           4        72     1
D61V36, multiclass
             clus
vv            10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 28                 72
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V37, continuous
D61V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  10Q LOSS MUTATED         2        0         0         1        9        16
  10Q LOSS WILD-TYPE       3        1         1         0       25        61
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  10Q LOSS MUTATED           9        1         4          2          1
  10Q LOSS WILD-TYPE        28        3         4          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  10Q LOSS MUTATED          10         0          2         13         2
  10Q LOSS WILD-TYPE        34         1          1         29         5
                    vv
clus                 STAGE IVB
  10Q LOSS MUTATED           1
  10Q LOSS WILD-TYPE        11
D61V39, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  9                 25
  STAGE IB1                16                 61
  STAGE IB2                 9                 28
  STAGE II                  1                  3
  STAGE IIA                 4                  4
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                10                 34
  STAGE III                 0                  1
  STAGE IIIA                2                  1
  STAGE IIIB               13                 29
  STAGE IVA                 2                  5
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    70  26
  11P LOSS WILD-TYPE 141  41
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                96                182 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                26                 41 
$`11P LOSS MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1BK TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M7 
       49.48        18.74       177.04        19.86        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A2LV 
       30.21        38.99        35.61         0.46        20.91        73.45 
TCGA-C5-A2LZ TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CL TCGA-C5-A7UH TCGA-C5-A7UI 
      100.14       210.67       154.32        15.48       131.11        94.95 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
        2.73        50.99       146.86        99.91        23.51        27.52 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 
       87.75        36.76        95.67        40.87        24.56        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A97N 
       26.01         0.30         7.46        27.25        27.22         0.36 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2RA TCGA-EK-A2RK TCGA-EK-A3GJ 
        1.51         0.43         0.59        40.96         0.43         0.10 
TCGA-EK-A3GM TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB TCGA-IR-A3LA 
        0.76        20.35        23.84        20.98        16.14       137.16 
TCGA-IR-A3LC TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-LP-A4AU 
      129.37        29.85        24.56        21.44        20.48        11.28 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA43 
       12.49         0.82        13.35        22.52        19.56        11.38 
TCGA-MU-A51Y TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       28.08        54.81        35.05         2.96        16.41         9.04 
TCGA-Q1-A73Q TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH 
        9.34        19.59        11.67        12.16        10.03        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q9 TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Y 
       23.97        19.96        53.59        11.51        59.18         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9UD 
       33.37        40.14        55.50        51.32        50.47        24.30 
TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       45.11        14.53        47.47        15.85        14.53         3.42 
TCGA-VS-A9V0 TCGA-VS-A9V3 TCGA-XS-A8TJ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZX-AA5X 
       18.84        17.75        29.26         0.69         1.41         3.91 

$`11P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        57.04        23.67        11.44        68.84 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 
       36.56       144.16       173.29        82.85         5.46        67.46 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       35.01        57.73        53.16         2.43        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        73.18        83.05        78.35        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK 
       52.01        18.02        17.85        20.42       101.82       134.33 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X5 
       20.35       147.35        17.19       155.77         9.34        13.61 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       45.83         8.35        20.81        20.91        14.73         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VL 
       95.11        82.06        44.94        63.98        58.88        55.63 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       69.96        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO 
       25.02        36.89        26.40        24.82        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       25.91        27.29        24.00        13.48        12.59        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2R8 
       26.27         6.64        19.27         0.39         0.36         1.45 
TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK 
        0.13         4.31         0.10        47.77         0.53         0.49 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03         7.92        15.22        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       15.55         1.22        19.04        16.11        31.36        36.26 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
       26.14         1.48        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12        17.75        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH 
       14.93         9.44       147.39        66.81        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VL TCGA-JW-A69B 
       81.96        36.36        27.42         3.29        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
        8.28        18.15        21.11       209.59        44.61        20.91 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
        0.89         0.30        17.82        19.56         8.35         8.52 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       34.62        19.96        20.84        17.23        15.58        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73R TCGA-Q1-A73S 
       16.14        17.56        14.07        15.88        18.64        22.62 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EL 
       14.60        93.99        69.50        46.52        45.57        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       32.15        36.13        39.78        31.27        40.87        16.64 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 
       58.45        15.68        56.35        50.14        43.40        48.39 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UM 
       28.50        29.95        27.12        46.92         1.71        27.25 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 
       47.87        41.52        26.07        18.25        67.20         5.16 
TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ 
       18.25         4.34        16.24        15.42        26.01        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAXU 
       19.13         0.16 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.10               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            210.67             209.59 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            23.675             22.800 
[1] "0.1 - 210.7 (23.7)" "0.0 - 209.6 (22.8)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED   39 24 10  3
  11P LOSS WILD-TYPE 96 46 11  5
D62V3, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               39                 96
  T2               24                 46
  T3               10                 11
  T4                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   38 15
  11P LOSS WILD-TYPE 91 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     38   15
  11P LOSS WILD-TYPE   91   41
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               38                 91
  1               15                 41
[1] 2 2
[1] FALSE
D62V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   36  2
  11P LOSS WILD-TYPE 72  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     36    2
  11P LOSS WILD-TYPE   72    8
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               36                 72
  1                2                  8
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   19 45
  11P LOSS WILD-TYPE 36 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     19   45
  11P LOSS WILD-TYPE   36   78
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                19                 36
  YES               45                 78
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED               0                               91
  11P LOSS WILD-TYPE             6                              151
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11P LOSS MUTATED                                               1
  11P LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11P LOSS MUTATED                                     3
  11P LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11P LOSS MUTATED                                           1
  11P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11P LOSS MUTATED                                              4
  11P LOSS WILD-TYPE                                           13
D62V7, multiclass
                                               clus
vv                                              11P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            91
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 4
                                               clus
vv                                              11P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             151
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, continuous
D62V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  3    11
  11P LOSS WILD-TYPE                                5     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED                          11
  11P LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           1    65
  11P LOSS WILD-TYPE                                         1   137
D62V10, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  5
  ASIAN                                                   11                  8
  BLACK OR AFRICAN AMERICAN                               11                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  1
  WHITE                                                   65                137
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     8  52
  11P LOSS WILD-TYPE  15 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8   52
  11P LOSS WILD-TYPE   15  110
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 15
  NOT HISPANIC OR LATINO               52                110
[1] 2 2
[1] FALSE
D62V12, continuous
D62V13, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    57  34
  11P LOSS WILD-TYPE 126  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     57   34
  11P LOSS WILD-TYPE  126   40
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  TUMOR FREE               57                126
  WITH TUMOR               34                 40
[1] 2 2
[1] FALSE
                    vv
clus                 G1 G2 G3 G4 GX
  11P LOSS MUTATED    4 37 49  0  7
  11P LOSS WILD-TYPE 14 92 66  1 17
D62V14, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  G1                4                 14
  G2               37                 92
  G3               49                 66
  G4                0                  1
  GX                7                 17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V15, continuous
D62V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11P LOSS MUTATED                                            10
  11P LOSS WILD-TYPE                                          28
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  11P LOSS MUTATED                                        3
  11P LOSS WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  11P LOSS MUTATED                                                 1
  11P LOSS WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11P LOSS MUTATED               25                  52
  11P LOSS WILD-TYPE             37                  91
D62V17, multiclass
                                                 clus
vv                                                11P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   10
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                25
  LIFELONG NON-SMOKER                                           52
                                                 clus
vv                                                11P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     28
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  37
  LIFELONG NON-SMOKER                                             91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V18, continuous
D62V19, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    7  0
  11P LOSS WILD-TYPE 18  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      7    0
  11P LOSS WILD-TYPE   18    3
                         clus
vv                        11P LOSS MUTATED 11P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   7                 18
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D62V20, continuous
D62V21, continuous
D62V22, continuous
D62V23, continuous
D62V24, continuous
D62V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  11P LOSS MUTATED                                     0
  11P LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  11P LOSS MUTATED                                     2
  11P LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  11P LOSS MUTATED                        14                       1
  11P LOSS WILD-TYPE                      22                       0
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11P LOSS MUTATED                         2
  11P LOSS WILD-TYPE                       6
D62V26, multiclass
                                     clus
vv                                    11P LOSS MUTATED 11P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  5
  OTHER LOCATION, SPECIFY                           14                 22
  POSITIVE BLADDER MARGIN                            1                  0
  POSITIVE VAGINAL MARGIN                            2                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  11P LOSS MUTATED                                               1
  11P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  11P LOSS MUTATED                                               10
  11P LOSS WILD-TYPE                                             15
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11P LOSS MUTATED                                                                                  37
  11P LOSS WILD-TYPE                                                                                45
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11P LOSS MUTATED                                                                                             30
  11P LOSS WILD-TYPE                                                                                           91
D62V27, multiclass
                                                                                              clus
vv                                                                                             11P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          37
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               30
                                                                                              clus
vv                                                                                             11P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               15
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V28, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   23 18
  11P LOSS WILD-TYPE 48 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     23   18
  11P LOSS WILD-TYPE   48   56
         clus
vv        11P LOSS MUTATED 11P LOSS WILD-TYPE
  ABSENT                23                 48
  PRESENT               18                 56
[1] 2 2
[1] FALSE
D62V29, continuous
D62V30, continuous
D62V31, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   17 37
  11P LOSS WILD-TYPE 32 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     17   37
  11P LOSS WILD-TYPE   32   80
                                          clus
vv                                         11P LOSS MUTATED 11P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   17                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               37                 80
[1] 2 2
[1] FALSE
D62V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11P LOSS MUTATED              3          14         34
  11P LOSS WILD-TYPE           12          40         51
D62V33, multiclass
              clus
vv             11P LOSS MUTATED 11P LOSS WILD-TYPE
  CURRENT USER                3                 12
  FORMER USER                14                 40
  NEVER USED                 34                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V34, continuous
D62V35, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   26  7
  11P LOSS WILD-TYPE 66 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     26    7
  11P LOSS WILD-TYPE   66   11
         clus
vv        11P LOSS MUTATED 11P LOSS WILD-TYPE
  ABSENT                26                 66
  PRESENT                7                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  11P LOSS MUTATED             0        35     0
  11P LOSS WILD-TYPE           5        65     2
D62V36, multiclass
             clus
vv            11P LOSS MUTATED 11P LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 35                 65
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V37, continuous
D62V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  11P LOSS MUTATED         2        0         0         1       17        23
  11P LOSS WILD-TYPE       3        1         1         0       17        54
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  11P LOSS MUTATED           5        2         2          3          2
  11P LOSS WILD-TYPE        32        2         6          2          5
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  11P LOSS MUTATED          17         0          2         17         3
  11P LOSS WILD-TYPE        27         1          1         25         4
                    vv
clus                 STAGE IVB
  11P LOSS MUTATED           1
  11P LOSS WILD-TYPE        11
D62V39, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                 17                 17
  STAGE IB1                23                 54
  STAGE IB2                 5                 32
  STAGE II                  2                  2
  STAGE IIA                 2                  6
  STAGE IIA1                3                  2
  STAGE IIA2                2                  5
  STAGE IIB                17                 27
  STAGE III                 0                  1
  STAGE IIIA                2                  1
  STAGE IIIB               17                 25
  STAGE IVA                 3                  4
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    83  30
  11Q LOSS WILD-TYPE 128  37
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               113                165 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                 37 
$`11Q LOSS MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
       49.48        68.84        18.74        31.40        46.32        30.21 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML 
       53.16        38.99        35.61         0.46         2.43        20.91 
TCGA-C5-A2LV TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CL 
       73.45       100.14        33.24       210.67       154.32        15.48 
TCGA-C5-A7CM TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8XK 
       20.35       131.11         2.73        45.83       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VN 
       23.51        27.52        82.06        87.75        36.76        95.67 
TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E 
       16.83        40.87        24.56        31.73        26.01         7.46 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG 
       27.25        27.22        13.48         0.36        12.59         1.51 
TCGA-EK-A2PI TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RK 
       19.27         0.59         0.13        40.96         0.10         0.43 
TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.10        20.35        19.79         8.32        20.98        26.14 
TCGA-FU-A3WB TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-JW-A5VK 
       16.14       137.16        66.81       129.37        81.96        20.48 
TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       11.28        12.49         0.82        13.35        22.52        19.56 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       11.38        28.08        34.62        54.81        35.05        20.84 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73Q 
        2.96        16.41         9.04        17.56        15.88         9.34 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EG 
       19.59        11.67        93.99        12.16        10.03        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 
       32.42        23.97        19.96        65.49        32.15        53.59 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A957 TCGA-VS-A959 
       11.51        59.18        33.37        40.14        55.50        51.32 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UP 
       43.40        48.39        24.30        45.11        14.53        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9V0 TCGA-VS-A9V3 
       41.52        15.85        14.53         3.42        18.84        17.75 
TCGA-XS-A8TJ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26         0.69         1.41         0.16         3.91 

$`11Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI 
       17.52        17.82        57.04        23.67        11.44        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       67.46        35.01        57.73        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE 
       73.18        83.05        78.35        38.43        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7UC 
       17.85        20.42       101.82       134.33       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XI 
      155.77        94.95         9.34        13.61        50.99         8.35 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL 
       20.81        20.91        14.73         1.12        95.11        44.94 
TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A7WF 
       63.98        58.88        55.63        69.96        22.98        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52         8.28        39.55        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S 
       31.36        13.05        25.02        36.89        26.40         0.30 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX 
       24.82        14.89        26.79        25.91        27.29        24.00 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 
       60.72        26.27         6.64         0.39         0.43         0.36 
TCGA-EK-A2R8 TCGA-EK-A2RC TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GM 
        1.45         4.31        47.77         0.53         0.49         0.76 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A8YF TCGA-FU-A23K 
        0.03         7.92        15.22        14.70        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX 
       23.84        19.04        16.11        31.36        36.26         1.48 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA 
       28.31        14.01        35.44        10.55         1.12        17.75 
TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
       25.41        16.57        21.67        20.78        14.93         9.44 
TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      147.39        96.95        78.71        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        21.44        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW 
       18.15        21.11       209.59        44.61        20.91         0.89 
TCGA-LP-A5U2 TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A8JM 
        0.30        17.82        19.56         8.35         8.52        19.96 
TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73O TCGA-Q1-A73R 
       17.23        15.58        15.95        16.14        14.07        18.64 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8QA TCGA-VS-A8QH 
       22.62        14.60        69.50        46.52        36.13        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 TCGA-VS-A953 
       31.27        40.87        16.64         4.73        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       56.35        50.14        50.47        28.50        29.95        27.12 
TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UR TCGA-VS-A9UY 
       46.92         1.71        27.25        47.87        26.07        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 
       67.20         5.16        18.25         4.34        16.24        15.42 
TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       26.01        67.59        19.13 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.10               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            210.67             209.59 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             23.97              22.62 
[1] "0.1 - 210.7 (24.0)" "0.0 - 209.6 (22.6)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED   51 23 10  4
  11Q LOSS WILD-TYPE 84 47 11  4
D63V3, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               51                 84
  T2               23                 47
  T3               10                 11
  T4                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   44 20
  11Q LOSS WILD-TYPE 85 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     44   20
  11Q LOSS WILD-TYPE   85   36
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               44                 85
  1               20                 36
[1] 2 2
[1] FALSE
D63V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   41  4
  11Q LOSS WILD-TYPE 67  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     41    4
  11Q LOSS WILD-TYPE   67    6
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               41                 67
  1                4                  6
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   21 54
  11Q LOSS WILD-TYPE 34 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     21   54
  11Q LOSS WILD-TYPE   34   69
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                21                 34
  YES               54                 69
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED               0                              102
  11Q LOSS WILD-TYPE             6                              140
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11Q LOSS MUTATED                                               1
  11Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11Q LOSS MUTATED                                     6
  11Q LOSS WILD-TYPE                                  15
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11Q LOSS MUTATED                                           1
  11Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11Q LOSS MUTATED                                              5
  11Q LOSS WILD-TYPE                                           12
D63V7, multiclass
                                               clus
vv                                              11Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                           102
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 5
                                               clus
vv                                              11Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             140
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, continuous
D63V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  2    12
  11Q LOSS WILD-TYPE                                6     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED                          12
  11Q LOSS WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           1    75
  11Q LOSS WILD-TYPE                                         1   127
D63V10, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                   12                  7
  BLACK OR AFRICAN AMERICAN                               12                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  1
  WHITE                                                   75                127
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     6  62
  11Q LOSS WILD-TYPE  17 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6   62
  11Q LOSS WILD-TYPE   17  100
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 17
  NOT HISPANIC OR LATINO               62                100
[1] 2 2
[1] FALSE
D63V12, continuous
D63V13, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    65  38
  11Q LOSS WILD-TYPE 118  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     65   38
  11Q LOSS WILD-TYPE  118   36
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  TUMOR FREE               65                118
  WITH TUMOR               38                 36
[1] 2 2
[1] FALSE
                    vv
clus                 G1 G2 G3 G4 GX
  11Q LOSS MUTATED    6 47 50  0  9
  11Q LOSS WILD-TYPE 12 82 65  1 15
D63V14, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  G1                6                 12
  G2               47                 82
  G3               50                 65
  G4                0                  1
  GX                9                 15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V15, continuous
D63V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11Q LOSS MUTATED                                            16
  11Q LOSS WILD-TYPE                                          22
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  11Q LOSS MUTATED                                        6
  11Q LOSS WILD-TYPE                                      3
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  11Q LOSS MUTATED                                                 1
  11Q LOSS WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11Q LOSS MUTATED               25                  55
  11Q LOSS WILD-TYPE             37                  88
D63V17, multiclass
                                                 clus
vv                                                11Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                25
  LIFELONG NON-SMOKER                                           55
                                                 clus
vv                                                11Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     22
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  37
  LIFELONG NON-SMOKER                                             88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V18, continuous
D63V19, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    9  1
  11Q LOSS WILD-TYPE 16  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      9    1
  11Q LOSS WILD-TYPE   16    2
                         clus
vv                        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D63V20, continuous
D63V21, continuous
D63V22, continuous
D63V23, continuous
D63V24, continuous
D63V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  11Q LOSS MUTATED                                     0
  11Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  11Q LOSS MUTATED                                     2
  11Q LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  11Q LOSS MUTATED                        15                       1
  11Q LOSS WILD-TYPE                      21                       0
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11Q LOSS MUTATED                         2
  11Q LOSS WILD-TYPE                       6
D63V26, multiclass
                                     clus
vv                                    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  5
  OTHER LOCATION, SPECIFY                           15                 21
  POSITIVE BLADDER MARGIN                            1                  0
  POSITIVE VAGINAL MARGIN                            2                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  11Q LOSS MUTATED                                               1
  11Q LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  11Q LOSS MUTATED                                               13
  11Q LOSS WILD-TYPE                                             12
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11Q LOSS MUTATED                                                                                  44
  11Q LOSS WILD-TYPE                                                                                38
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11Q LOSS MUTATED                                                                                             35
  11Q LOSS WILD-TYPE                                                                                           86
D63V27, multiclass
                                                                                              clus
vv                                                                                             11Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             13
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          44
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               35
                                                                                              clus
vv                                                                                             11Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               12
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            38
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V28, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   23 30
  11Q LOSS WILD-TYPE 48 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     23   30
  11Q LOSS WILD-TYPE   48   44
         clus
vv        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ABSENT                23                 48
  PRESENT               30                 44
[1] 2 2
[1] FALSE
D63V29, continuous
D63V30, continuous
D63V31, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   19 43
  11Q LOSS WILD-TYPE 30 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     19   43
  11Q LOSS WILD-TYPE   30   74
                                          clus
vv                                         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   19                 30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               43                 74
[1] 2 2
[1] FALSE
D63V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11Q LOSS MUTATED              5          18         35
  11Q LOSS WILD-TYPE           10          36         50
D63V33, multiclass
              clus
vv             11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CURRENT USER                5                 10
  FORMER USER                18                 36
  NEVER USED                 35                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V34, continuous
D63V35, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   31  9
  11Q LOSS WILD-TYPE 61  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     31    9
  11Q LOSS WILD-TYPE   61    9
         clus
vv        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ABSENT                31                 61
  PRESENT                9                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  11Q LOSS MUTATED             1        40     0
  11Q LOSS WILD-TYPE           4        60     2
D63V36, multiclass
             clus
vv            11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 40                 60
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V37, continuous
D63V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  11Q LOSS MUTATED         3        0         1         1       17        32
  11Q LOSS WILD-TYPE       2        1         0         0       17        45
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  11Q LOSS MUTATED           8        2         1          2          3
  11Q LOSS WILD-TYPE        29        2         7          3          4
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  11Q LOSS MUTATED          15         0          2         19         3
  11Q LOSS WILD-TYPE        29         1          1         23         4
                    vv
clus                 STAGE IVB
  11Q LOSS MUTATED           3
  11Q LOSS WILD-TYPE         9
D63V39, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                  0                  1
  STAGE IA1                 1                  0
  STAGE IA2                 1                  0
  STAGE IB                 17                 17
  STAGE IB1                32                 45
  STAGE IB2                 8                 29
  STAGE II                  2                  2
  STAGE IIA                 1                  7
  STAGE IIA1                2                  3
  STAGE IIA2                3                  4
  STAGE IIB                15                 29
  STAGE III                 0                  1
  STAGE IIIA                2                  1
  STAGE IIIB               19                 23
  STAGE IVA                 3                  4
  STAGE IVB                 3                  9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    31   8
  12P LOSS WILD-TYPE 180  59
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                39                239 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                 59 
$`12P LOSS MUTATED`
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A2LV 
      177.04       173.29        30.21        35.01        40.93        73.45 
TCGA-C5-A2M1 TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-DG-A2KJ TCGA-DS-A0VK TCGA-DS-A0VL 
       38.43       131.11         2.73        95.11        36.76        55.63 
TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RK 
       40.87        24.56        26.01         1.51         0.59         0.43 
TCGA-FU-A2QG TCGA-FU-A40J TCGA-HG-A9SC TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JX-A3PZ 
       19.04        14.01        16.57        78.71        29.85        21.11 
TCGA-LP-A4AX TCGA-MA-AA3X TCGA-MA-AA43 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-VS-A8QF 
       12.49        19.56        11.38        16.41         9.04        59.18 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A9U7 TCGA-VS-A9UB TCGA-VS-A9UI TCGA-VS-A9UR 
       33.37        40.14        48.39        29.95        45.11        26.07 
TCGA-VS-A9V2 TCGA-VS-A9V5 TCGA-ZJ-AAX4 
       18.25        16.24         0.69 

$`12P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BM TCGA-C5-A1BN 
       68.84        18.74        36.56       144.16        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1MF 
       19.86        67.46        31.40        46.32        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP 
       38.99        35.61         0.46         2.43        20.91         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 
       44.22        73.18        83.05        78.35       100.14        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       52.01        18.02        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH 
      155.77        94.95         9.34        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35       146.86        99.91        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91        14.73         1.12        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       87.75        58.88        69.96        95.67        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18        17.52         8.28        39.55        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       31.73         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
        0.36        12.59        60.72        26.27         6.64        19.27 
TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.39         0.43         0.36         1.45         0.13        40.96 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK 
        4.31         0.10        47.77         0.53         0.10         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.76         0.03        20.35         7.92        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       19.79         8.32        15.55         1.22        23.84        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
       31.36        36.26        20.98        26.14         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       28.31        35.44        10.55         1.12        17.75        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
       66.81       129.37        96.95        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
        3.29        24.56        21.44        20.48        15.58        28.37 
TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
        8.28        18.15       209.59        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y 
        0.89         0.30         0.82        13.35        22.52        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         8.35         8.52        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 
       54.81        35.05        20.84        17.23         2.96        15.58 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
       15.95        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       23.97        19.96        65.49        32.15        53.59        36.13 
TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        39.78        31.27        40.87        16.64         4.73 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       58.45        15.68        56.35        55.50        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       50.47        43.40        28.50        27.12        24.30        46.92 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ 
        1.71        14.53        27.25        47.87        47.47        41.52 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       15.85        14.53         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
        5.16        17.75         4.34        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.43               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            177.04             210.67 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             29.85              21.67 
[1] "0.4 - 177.0 (29.9)" "0.0 - 210.7 (21.7)"
[1] "hr=" "1.4"
D64V2, continuous
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED    17  11   4   0
  12P LOSS WILD-TYPE 118  59  17   8
D64V3, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               17                118
  T2               11                 59
  T3                4                 17
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    17   7
  12P LOSS WILD-TYPE 112  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     17    7
  12P LOSS WILD-TYPE  112   49
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               17                112
  1                7                 49
[1] 2 2
[1] FALSE
D64V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   15  0
  12P LOSS WILD-TYPE 93 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     15    0
  12P LOSS WILD-TYPE   93   10
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               15                 93
  1                0                 10
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     5  17
  12P LOSS WILD-TYPE  50 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5   17
  12P LOSS WILD-TYPE   50  106
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 5                 50
  YES               17                106
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED               1                               33
  12P LOSS WILD-TYPE             5                              209
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12P LOSS MUTATED                                               0
  12P LOSS WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12P LOSS MUTATED                                     3
  12P LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12P LOSS MUTATED                                           0
  12P LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12P LOSS MUTATED                                              3
  12P LOSS WILD-TYPE                                           14
D64V7, multiclass
                                               clus
vv                                              12P LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            33
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 3
                                               clus
vv                                              12P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             209
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, continuous
D64V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     1
  12P LOSS WILD-TYPE                                8    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED                           5
  12P LOSS WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           0    30
  12P LOSS WILD-TYPE                                         2   172
D64V10, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                5                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   30                172
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  22
  12P LOSS WILD-TYPE  22 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   22
  12P LOSS WILD-TYPE   22  140
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 22
  NOT HISPANIC OR LATINO               22                140
[1] 2 2
[1] FALSE
D64V12, continuous
D64V13, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    27   9
  12P LOSS WILD-TYPE 156  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     27    9
  12P LOSS WILD-TYPE  156   65
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  TUMOR FREE               27                156
  WITH TUMOR                9                 65
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  12P LOSS MUTATED     0  18  18   1   3
  12P LOSS WILD-TYPE  18 111  97   0  21
D64V14, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  G1                0                 18
  G2               18                111
  G3               18                 97
  G4                1                  0
  GX                3                 21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V15, continuous
D64V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  12P LOSS MUTATED                                             8
  12P LOSS WILD-TYPE                                          30
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  12P LOSS MUTATED                                        0
  12P LOSS WILD-TYPE                                      9
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  12P LOSS MUTATED                                                 0
  12P LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12P LOSS MUTATED                4                  23
  12P LOSS WILD-TYPE             58                 120
D64V17, multiclass
                                                 clus
vv                                                12P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                           23
                                                 clus
vv                                                12P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  58
  LIFELONG NON-SMOKER                                            120
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V18, continuous
D64V19, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    4  0
  12P LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    0
  12P LOSS WILD-TYPE   21    3
                         clus
vv                        12P LOSS MUTATED 12P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D64V20, continuous
D64V21, continuous
D64V22, continuous
D64V23, continuous
D64V24, continuous
D64V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  12P LOSS MUTATED                                     0
  12P LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  12P LOSS MUTATED                                     1
  12P LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  12P LOSS MUTATED                         7                       0
  12P LOSS WILD-TYPE                      29                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12P LOSS MUTATED                         3
  12P LOSS WILD-TYPE                       5
D64V26, multiclass
                                     clus
vv                                    12P LOSS MUTATED 12P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                            7                 29
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  12P LOSS MUTATED                                               1
  12P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12P LOSS MUTATED                                                4
  12P LOSS WILD-TYPE                                             21
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12P LOSS MUTATED                                                                                  11
  12P LOSS WILD-TYPE                                                                                71
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12P LOSS MUTATED                                                                                             18
  12P LOSS WILD-TYPE                                                                                          103
D64V27, multiclass
                                                                                              clus
vv                                                                                             12P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              4
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               18
                                                                                              clus
vv                                                                                             12P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               21
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            71
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V28, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    9  9
  12P LOSS WILD-TYPE 62 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      9    9
  12P LOSS WILD-TYPE   62   65
         clus
vv        12P LOSS MUTATED 12P LOSS WILD-TYPE
  ABSENT                 9                 62
  PRESENT                9                 65
[1] 2 2
[1] FALSE
D64V29, continuous
D64V30, continuous
D64V31, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     7  13
  12P LOSS WILD-TYPE  42 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      7   13
  12P LOSS WILD-TYPE   42  104
                                          clus
vv                                         12P LOSS MUTATED 12P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    7                 42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               13                104
[1] 2 2
[1] FALSE
D64V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12P LOSS MUTATED              1           9         18
  12P LOSS WILD-TYPE           14          45         67
D64V33, multiclass
              clus
vv             12P LOSS MUTATED 12P LOSS WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 9                 45
  NEVER USED                 18                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V34, continuous
D64V35, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   15  0
  12P LOSS WILD-TYPE 77 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     15    0
  12P LOSS WILD-TYPE   77   18
         clus
vv        12P LOSS MUTATED 12P LOSS WILD-TYPE
  ABSENT                15                 77
  PRESENT                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  12P LOSS MUTATED             1        14     0
  12P LOSS WILD-TYPE           4        86     2
D64V36, multiclass
             clus
vv            12P LOSS MUTATED 12P LOSS WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 14                 86
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V37, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MA-AA3W         TCGA-MA-AA3Z         TCGA-MA-AA42 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ZX-AA5X 
"12P LOSS WILD-TYPE" 
D64V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  12P LOSS MUTATED         1        0         0         1        7        10
  12P LOSS WILD-TYPE       4        1         1         0       27        67
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  12P LOSS MUTATED           1        1         1          1          0
  12P LOSS WILD-TYPE        36        3         7          4          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  12P LOSS MUTATED           8         0          1          6         0
  12P LOSS WILD-TYPE        36         1          2         36         7
                    vv
clus                 STAGE IVB
  12P LOSS MUTATED           0
  12P LOSS WILD-TYPE        12
D64V39, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  7                 27
  STAGE IB1                10                 67
  STAGE IB2                 1                 36
  STAGE II                  1                  3
  STAGE IIA                 1                  7
  STAGE IIA1                1                  4
  STAGE IIA2                0                  7
  STAGE IIB                 8                 36
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                6                 36
  STAGE IVA                 0                  7
  STAGE IVB                 0                 12
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    11   4
  12Q LOSS WILD-TYPE 200  63
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                263 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 63 
$`12Q LOSS MUTATED`
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 
       30.21        35.01        40.93       131.11        13.61         2.73 
TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2RK TCGA-FU-A770 TCGA-MA-AA3X TCGA-VS-A950 
        1.51         0.59         0.43         1.12        19.56        40.14 
TCGA-VS-A9UI TCGA-VS-A9UR TCGA-ZJ-AAX4 
       45.11        26.07         0.69 

$`12Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       57.73        53.16        38.99        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       20.91         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43        33.24        52.01        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       210.67       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
       15.48        20.35       147.35        17.19       155.77        94.95 
TCGA-C5-A7X3 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        9.34        50.99        45.83         8.35       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        14.73         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       95.11        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76        55.63        69.96        95.67        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       26.40        24.56        31.73        26.01         0.30        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 
       27.22        24.00        13.48         0.36        12.59        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 
       26.27         6.64        19.27         0.39         0.43         0.36 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL 
        1.45         0.13        40.96         4.31         0.10        47.77 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
        0.53         0.10         0.49         0.76         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF 
        7.92        15.22        14.70        19.79         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       20.98        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44        10.55        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      129.37        96.95        78.71        81.96        29.85        36.36 
TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       27.42         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       20.91        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       13.35        22.52        17.82        19.56         8.35         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       20.84        17.23         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH 
       12.16        69.50        10.03        46.52        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       23.97        19.96        65.49        32.15        53.59        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       11.51        59.18        39.78        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
        4.73        33.37        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL 
       29.95        27.12        24.30        46.92         1.71        14.53 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UT TCGA-VS-A9UU 
       27.25        47.87        47.47        41.52        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
        3.42        18.25        67.20        18.84         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       17.75         4.34        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.43               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            131.11             210.67 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             19.56              23.51 
[1] "0.4 - 131.1 (19.6)" "0.0 - 210.7 (23.5)"
[1] "hr=" "1.4"
D65V2, continuous
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED     2   5   3   0
  12Q LOSS WILD-TYPE 133  65  18   8
D65V3, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                2                133
  T2                5                 65
  T3                3                 18
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V4, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3   3
  12Q LOSS WILD-TYPE 126  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    3
  12Q LOSS WILD-TYPE  126   53
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                3                126
  1                3                 53
[1] 2 2
[1] FALSE
D65V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3   0
  12Q LOSS WILD-TYPE 105  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    0
  12Q LOSS WILD-TYPE  105   10
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                3                105
  1                0                 10
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0   7
  12Q LOSS WILD-TYPE  55 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    7
  12Q LOSS WILD-TYPE   55  116
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 0                 55
  YES                7                116
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED               0                               11
  12Q LOSS WILD-TYPE             6                              231
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12Q LOSS MUTATED                                               1
  12Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12Q LOSS MUTATED                                     1
  12Q LOSS WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12Q LOSS MUTATED                                           0
  12Q LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12Q LOSS MUTATED                                              2
  12Q LOSS WILD-TYPE                                           15
D65V7, multiclass
                                               clus
vv                                              12Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            11
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              12Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             231
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, continuous
D65V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                8    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED                           3
  12Q LOSS WILD-TYPE                        25
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0    11
  12Q LOSS WILD-TYPE                                         2   191
D65V10, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                3                 25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   11                191
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  10
  12Q LOSS WILD-TYPE  23 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   10
  12Q LOSS WILD-TYPE   23  152
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 23
  NOT HISPANIC OR LATINO               10                152
[1] 2 2
[1] FALSE
D65V12, continuous
D65V13, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     7   5
  12Q LOSS WILD-TYPE 176  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      7    5
  12Q LOSS WILD-TYPE  176   69
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  TUMOR FREE                7                176
  WITH TUMOR                5                 69
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  12Q LOSS MUTATED     0   5   8   0   2
  12Q LOSS WILD-TYPE  18 124 107   1  22
D65V14, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  G1                0                 18
  G2                5                124
  G3                8                107
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V15, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 42 
        TCGA-2W-A8YY         TCGA-BI-A0VR         TCGA-C5-A1BJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BQ         TCGA-C5-A1ME 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A2M2 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A7CM         TCGA-C5-A7CO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A8XH         TCGA-C5-A907         TCGA-DG-A2KK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-EK-A2RA         TCGA-EX-A69M 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3TX         TCGA-FU-A3WB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-HM-A4S6         TCGA-IR-A3L7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JX-A3Q0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-MA-AA43         TCGA-MU-A5YI         TCGA-MU-A8JM 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-Q1-A73S         TCGA-RA-A741 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-VS-A8QF         TCGA-VS-A94Z         TCGA-VS-A9V0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-VS-A9V4         TCGA-WL-A834         TCGA-ZJ-A8QR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ZJ-AAXA         TCGA-ZJ-AAXT         TCGA-ZJ-AB0I 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D65V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  12Q LOSS MUTATED                                             1
  12Q LOSS WILD-TYPE                                          37
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  12Q LOSS MUTATED                                        0
  12Q LOSS WILD-TYPE                                      9
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  12Q LOSS MUTATED                                                 0
  12Q LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12Q LOSS MUTATED                4                   6
  12Q LOSS WILD-TYPE             58                 137
D65V17, multiclass
                                                 clus
vv                                                12Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                            6
                                                 clus
vv                                                12Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     37
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  58
  LIFELONG NON-SMOKER                                            137
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V18, continuous
D65V19, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    3  0
  12Q LOSS WILD-TYPE 22  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    0
  12Q LOSS WILD-TYPE   22    3
                         clus
vv                        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   3                 22
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D65V20, continuous
D65V21, continuous
D65V22, continuous
D65V23, continuous
D65V24, continuous
D65V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  12Q LOSS MUTATED                                     0
  12Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  12Q LOSS MUTATED                                     0
  12Q LOSS WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  12Q LOSS MUTATED                         3                       0
  12Q LOSS WILD-TYPE                      33                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12Q LOSS MUTATED                         1
  12Q LOSS WILD-TYPE                       7
D65V26, multiclass
                                     clus
vv                                    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            3                 33
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  12Q LOSS MUTATED                                               1
  12Q LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12Q LOSS MUTATED                                                0
  12Q LOSS WILD-TYPE                                             25
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12Q LOSS MUTATED                                                                                   5
  12Q LOSS WILD-TYPE                                                                                77
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12Q LOSS MUTATED                                                                                              4
  12Q LOSS WILD-TYPE                                                                                          117
D65V27, multiclass
                                                                                              clus
vv                                                                                             12Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              0
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                4
                                                                                              clus
vv                                                                                             12Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               25
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            77
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V28, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    3  3
  12Q LOSS WILD-TYPE 68 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    3
  12Q LOSS WILD-TYPE   68   71
         clus
vv        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ABSENT                 3                 68
  PRESENT                3                 71
[1] 2 2
[1] FALSE
D65V29, continuous
D65V30, continuous
D65V31, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3   3
  12Q LOSS WILD-TYPE  46 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    3
  12Q LOSS WILD-TYPE   46  114
                                          clus
vv                                         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 46
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                3                114
[1] 2 2
[1] FALSE
D65V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12Q LOSS MUTATED              0           4          5
  12Q LOSS WILD-TYPE           15          50         80
D65V33, multiclass
              clus
vv             12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CURRENT USER                0                 15
  FORMER USER                 4                 50
  NEVER USED                  5                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V34, continuous
D65V35, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    3  0
  12Q LOSS WILD-TYPE 89 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    0
  12Q LOSS WILD-TYPE   89   18
         clus
vv        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ABSENT                 3                 89
  PRESENT                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  12Q LOSS MUTATED             1         6     0
  12Q LOSS WILD-TYPE           4        94     2
D65V36, multiclass
             clus
vv            12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                  6                 94
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V37, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-MA-AA3W         TCGA-MA-AA3Z         TCGA-MA-AA42 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ZX-AA5X 
"12Q LOSS WILD-TYPE" 
D65V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  12Q LOSS MUTATED         0        0         0         1        0         3
  12Q LOSS WILD-TYPE       5        1         1         0       34        74
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  12Q LOSS MUTATED           0        1         1          0          0
  12Q LOSS WILD-TYPE        37        3         7          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  12Q LOSS MUTATED           2         0          1          4         0
  12Q LOSS WILD-TYPE        42         1          2         38         7
                    vv
clus                 STAGE IVB
  12Q LOSS MUTATED           1
  12Q LOSS WILD-TYPE        11
D65V39, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  0                 34
  STAGE IB1                 3                 74
  STAGE IB2                 0                 37
  STAGE II                  1                  3
  STAGE IIA                 1                  7
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 2                 42
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                4                 38
  STAGE IVA                 0                  7
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    54  20
  13Q LOSS WILD-TYPE 157  47
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                74                204 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                 47 
$`13Q LOSS MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BF TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1MH 
       49.48        57.04        18.74        82.85        31.40        38.99 
TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7CO 
       73.18        83.05        52.01        18.02       154.32       147.35 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-DG-A2KJ 
      155.77        94.95         9.34       146.86        99.91        95.11 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A439 
       69.96        95.67        22.98        40.87        25.02        31.73 
TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2R8 
       12.59        26.27        19.27         0.39         0.36         1.45 
TCGA-EK-A2RA TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI 
       40.96         0.10         0.43        20.35        23.84        20.98 
TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A4S6 TCGA-HM-A6W2 
       26.14        10.55        25.41        16.57        14.93         9.44 
TCGA-IR-A3L7 TCGA-JW-A5VK TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-LP-A4AU TCGA-LP-A4AW 
      147.39        20.48        18.15        21.11        11.28         0.89 
TCGA-LP-A4AX TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EC 
       12.49         9.04        19.59        12.16        10.03        46.52 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94Y 
       32.42        23.97        19.96        59.18        31.27         4.73 
TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A9U5 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL 
       15.68        55.50        50.47        24.30        45.11        14.53 
TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UT TCGA-VS-A9UU TCGA-WL-A834 TCGA-XS-A8TJ 
       27.25        47.47        15.85        14.53        26.01        29.26 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       19.13         0.69 

$`13Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       17.52        17.82        23.67        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29         5.46        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       46.32        30.21        35.01        57.73        53.16        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF 
       73.45        78.35       100.14        38.43        33.24        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       210.67       101.82       134.33        15.48        20.35 
TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH 
       17.19       131.11        13.61         2.73        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
        8.35        23.51        27.52        20.81        20.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1.12        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       36.76        55.63        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       36.89        26.40        24.56        26.01         0.30        24.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        7.46        14.89        26.79        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2IP 
       27.22        24.00        13.48         0.36        60.72         6.64 
TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RL 
        1.51         0.43         0.59         0.13         4.31        47.77 
TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H6 
        0.53         0.10         0.49         0.76         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       15.22        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB 
       19.04        16.11        31.36        36.26         1.48        16.14 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HM-A3JJ 
       28.31        14.01        35.44         1.12        17.75        21.67 
TCGA-HM-A3JK TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
       20.78       137.16        66.81       129.37        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       81.96        29.85        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       21.44        15.58        28.37         8.28       209.59        44.61 
TCGA-JX-A5QV TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X 
       20.91         0.30         0.82        13.35        22.52        19.56 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         8.35         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       34.62        19.96        54.81        35.05        20.84        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96        15.58        16.41        15.95        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-RA-A741 
       14.07        15.88         9.34        18.64        22.62        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EL TCGA-VS-A8Q8 
       11.67        93.99        69.50        45.57        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A94W TCGA-VS-A94X 
       53.59        36.13        11.51        39.78        40.87        16.64 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 
       33.37        40.14        58.45        56.35        50.14        51.32 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH 
       43.40        48.39        28.50        29.95        27.12        46.92 
TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UV TCGA-VS-A9UY 
        1.71        47.87        41.52        26.07         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       67.20        18.84         5.16        18.25        17.75         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-ZJ-A8QQ TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       16.24        15.42        67.59         1.41         0.16         3.91 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.10               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            155.77             210.67 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            24.135             22.095 
[1] "0.1 - 155.8 (24.1)" "0.0 - 210.7 (22.1)"
[1] "hr=" "1"  
D66V2, continuous
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED    31  19  10   1
  13Q LOSS WILD-TYPE 104  51  11   7
D66V3, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               31                104
  T2               19                 51
  T3               10                 11
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V4, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    26  20
  13Q LOSS WILD-TYPE 103  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     26   20
  13Q LOSS WILD-TYPE  103   36
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               26                103
  1               20                 36
[1] 2 2
[1] FALSE
D66V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   29  4
  13Q LOSS WILD-TYPE 79  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     29    4
  13Q LOSS WILD-TYPE   79    6
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               29                 79
  1                4                  6
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   12 38
  13Q LOSS WILD-TYPE 43 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     12   38
  13Q LOSS WILD-TYPE   43   85
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                12                 43
  YES               38                 85
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED               2                               75
  13Q LOSS WILD-TYPE             4                              167
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  13Q LOSS MUTATED                                               1
  13Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  13Q LOSS MUTATED                                     0
  13Q LOSS WILD-TYPE                                  21
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  13Q LOSS MUTATED                                           0
  13Q LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  13Q LOSS MUTATED                                              2
  13Q LOSS WILD-TYPE                                           15
D66V7, multiclass
                                               clus
vv                                              13Q LOSS MUTATED
  ADENOSQUAMOUS                                                2
  CERVICAL SQUAMOUS CELL CARCINOMA                            75
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              13Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  4
  CERVICAL SQUAMOUS CELL CARCINOMA                             167
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, continuous
D66V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     6
  13Q LOSS WILD-TYPE                                7    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED                           9
  13Q LOSS WILD-TYPE                        19
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           1    54
  13Q LOSS WILD-TYPE                                         1   148
D66V10, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    6                 13
  BLACK OR AFRICAN AMERICAN                                9                 19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  1
  WHITE                                                   54                148
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     3  45
  13Q LOSS WILD-TYPE  20 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3   45
  13Q LOSS WILD-TYPE   20  117
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 20
  NOT HISPANIC OR LATINO               45                117
[1] 2 2
[1] FALSE
D66V12, continuous
D66V13, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    50  19
  13Q LOSS WILD-TYPE 133  55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     50   19
  13Q LOSS WILD-TYPE  133   55
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  TUMOR FREE               50                133
  WITH TUMOR               19                 55
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  13Q LOSS MUTATED     4  26  39   0   8
  13Q LOSS WILD-TYPE  14 103  76   1  16
D66V14, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  G1                4                 14
  G2               26                103
  G3               39                 76
  G4                0                  1
  GX                8                 16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V15, continuous
D66V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  13Q LOSS MUTATED                                             8
  13Q LOSS WILD-TYPE                                          30
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  13Q LOSS MUTATED                                        5
  13Q LOSS WILD-TYPE                                      4
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  13Q LOSS MUTATED                                                 1
  13Q LOSS WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  13Q LOSS MUTATED               22                  30
  13Q LOSS WILD-TYPE             40                 113
D66V17, multiclass
                                                 clus
vv                                                13Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                22
  LIFELONG NON-SMOKER                                           30
                                                 clus
vv                                                13Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     30
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  40
  LIFELONG NON-SMOKER                                            113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V18, continuous
D66V19, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    9  0
  13Q LOSS WILD-TYPE 16  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    0
  13Q LOSS WILD-TYPE   16    3
                         clus
vv                        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D66V20, continuous
D66V21, continuous
D66V22, continuous
D66V23, continuous
D66V24, continuous
D66V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  13Q LOSS MUTATED                                     0
  13Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  13Q LOSS MUTATED                                     2
  13Q LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  13Q LOSS MUTATED                         9                       0
  13Q LOSS WILD-TYPE                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  13Q LOSS MUTATED                         3
  13Q LOSS WILD-TYPE                       5
D66V26, multiclass
                                     clus
vv                                    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  5
  OTHER LOCATION, SPECIFY                            9                 27
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  13Q LOSS MUTATED                                               0
  13Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  13Q LOSS MUTATED                                                8
  13Q LOSS WILD-TYPE                                             17
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  13Q LOSS MUTATED                                                                                  22
  13Q LOSS WILD-TYPE                                                                                60
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  13Q LOSS MUTATED                                                                                             30
  13Q LOSS WILD-TYPE                                                                                           91
D66V27, multiclass
                                                                                              clus
vv                                                                                             13Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          22
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               30
                                                                                              clus
vv                                                                                             13Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               17
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            60
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V28, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   12 25
  13Q LOSS WILD-TYPE 59 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     12   25
  13Q LOSS WILD-TYPE   59   49
         clus
vv        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ABSENT                12                 59
  PRESENT               25                 49
[1] 2 2
[1] FALSE
D66V29, continuous
D66V30, continuous
D66V31, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   13 32
  13Q LOSS WILD-TYPE 36 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     13   32
  13Q LOSS WILD-TYPE   36   85
                                          clus
vv                                         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   13                 36
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               32                 85
[1] 2 2
[1] FALSE
D66V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  13Q LOSS MUTATED              4          13         19
  13Q LOSS WILD-TYPE           11          41         66
D66V33, multiclass
              clus
vv             13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CURRENT USER                4                 11
  FORMER USER                13                 41
  NEVER USED                 19                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V34, continuous
D66V35, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   15  7
  13Q LOSS WILD-TYPE 77 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     15    7
  13Q LOSS WILD-TYPE   77   11
         clus
vv        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ABSENT                15                 77
  PRESENT                7                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  13Q LOSS MUTATED             0        30     1
  13Q LOSS WILD-TYPE           5        70     1
D66V36, multiclass
             clus
vv            13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 30                 70
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V37, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1ML         TCGA-C5-A1MN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-MA-AA3W         TCGA-MA-AA3Z         TCGA-MA-AA42 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ZX-AA5X 
"13Q LOSS WILD-TYPE" 
D66V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  13Q LOSS MUTATED         2        1         0         1       15        11
  13Q LOSS WILD-TYPE       3        0         1         0       19        66
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  13Q LOSS MUTATED           8        1         2          2          1
  13Q LOSS WILD-TYPE        29        3         6          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  13Q LOSS MUTATED          12         0          1         17         1
  13Q LOSS WILD-TYPE        32         1          2         25         6
                    vv
clus                 STAGE IVB
  13Q LOSS MUTATED           3
  13Q LOSS WILD-TYPE         9
D66V39, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  1                  0
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                 15                 19
  STAGE IB1                11                 66
  STAGE IB2                 8                 29
  STAGE II                  1                  3
  STAGE IIA                 2                  6
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                12                 32
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB               17                 25
  STAGE IVA                 1                  6
  STAGE IVB                 3                  9
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    23   6
  14Q LOSS WILD-TYPE 188  61
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                29                249 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 6                 61 
$`14Q LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE 
       23.67        57.73         0.46        83.05        38.43        18.02 
TCGA-C5-A7CM TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KJ TCGA-EA-A3Y4 TCGA-EA-A411 
       20.35        23.51        27.52        95.11        36.89        24.56 
TCGA-EA-A43B TCGA-EA-A78R TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EX-A8YF 
       26.01        13.48         1.51         0.39         0.59        15.55 
TCGA-FU-A23L TCGA-FU-A3TX TCGA-LP-A4AU TCGA-LP-A7HU TCGA-MA-AA42 TCGA-Q1-A5R2 
       23.84         1.48        11.28        13.35         8.52        16.41 
TCGA-UC-A7PG TCGA-VS-A8QH TCGA-VS-A959 TCGA-VS-A9V3 TCGA-VS-A9V4 
       12.16        39.78        51.32        17.75         4.34 

$`14Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML 
       35.01        53.16        38.99        35.61         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY 
       40.93         3.58        44.22        73.18        73.45        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
      100.14        33.24        52.01        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC 
      154.32       101.82       134.33        15.48       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
      155.77       131.11        94.95         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT 
       50.99        45.83         8.35       146.86        99.91        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91        14.73         1.12        82.06        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76        55.63        69.96        95.67 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       40.87        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       25.02        26.40        31.73         0.30        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        25.91        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       24.00         0.36        12.59        60.72        26.27         6.64 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
       19.27         0.43         0.36         1.45         0.13        40.96 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ 
        4.31         0.10         0.43        47.77         0.53         0.10 
TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.49         0.76         0.03        20.35         7.92        15.22 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70        19.79         8.32         1.22        19.04        16.11 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
       31.36        36.26        20.98        26.14        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA 
       14.01        35.44        10.55         1.12        17.75        25.41 
TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       16.57        21.67        20.78        14.93         9.44       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       129.37        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        28.37         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
      209.59        44.61        20.91         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
        0.82        22.52        19.56        17.82        19.56         8.35 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       20.84        17.23         2.96        15.58        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI 
       22.62        19.59        14.60        11.67        93.99        69.50 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ 
       10.03        46.52        45.57        32.42        23.97        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       65.49        32.15        53.59        36.13        11.51        59.18 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        40.87        16.64         4.73        33.37        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 
       58.45        15.68        56.35        55.50        50.14        50.47 
TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       43.40        48.39        28.50        29.95        27.12        24.30 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       46.92        45.11         1.71        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V5 
       18.25        67.20        18.84         5.16        18.25        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       15.42        26.01        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.39               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             95.11             210.67 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             18.02              24.00 
[1] "0.4 - 95.1 (18.0)"  "0.0 - 210.7 (24.0)"
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED    15   7   2   2
  14Q LOSS WILD-TYPE 120  63  19   6
D67V3, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               15                120
  T2                7                 63
  T3                2                 19
  T4                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V4, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    16   6
  14Q LOSS WILD-TYPE 113  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     16    6
  14Q LOSS WILD-TYPE  113   50
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               16                113
  1                6                 50
[1] 2 2
[1] FALSE
D67V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   17  0
  14Q LOSS WILD-TYPE 91 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     17    0
  14Q LOSS WILD-TYPE   91   10
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               17                 91
  1                0                 10
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     2  15
  14Q LOSS WILD-TYPE  53 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   15
  14Q LOSS WILD-TYPE   53  108
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 2                 53
  YES               15                108
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED               0                               27
  14Q LOSS WILD-TYPE             6                              215
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  14Q LOSS MUTATED                                               2
  14Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  14Q LOSS MUTATED                                     4
  14Q LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  14Q LOSS MUTATED                                           0
  14Q LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  14Q LOSS MUTATED                                              2
  14Q LOSS WILD-TYPE                                           15
D67V7, multiclass
                                               clus
vv                                              14Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            27
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              14Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             215
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  15
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, continuous
D67V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     3
  14Q LOSS WILD-TYPE                                8    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED                           1
  14Q LOSS WILD-TYPE                        27
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           0    26
  14Q LOSS WILD-TYPE                                         2   176
D67V10, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                1                 27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   26                176
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     2  19
  14Q LOSS WILD-TYPE  21 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   19
  14Q LOSS WILD-TYPE   21  143
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 21
  NOT HISPANIC OR LATINO               19                143
[1] 2 2
[1] FALSE
D67V12, continuous
D67V13, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    17   8
  14Q LOSS WILD-TYPE 166  66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     17    8
  14Q LOSS WILD-TYPE  166   66
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  TUMOR FREE               17                166
  WITH TUMOR                8                 66
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  14Q LOSS MUTATED     2  10  20   0   0
  14Q LOSS WILD-TYPE  16 119  95   1  24
D67V14, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  G1                2                 16
  G2               10                119
  G3               20                 95
  G4                0                  1
  GX                0                 24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V15, continuous
D67V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  14Q LOSS MUTATED                                             4
  14Q LOSS WILD-TYPE                                          34
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  14Q LOSS MUTATED                                        0
  14Q LOSS WILD-TYPE                                      9
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  14Q LOSS MUTATED                                                 0
  14Q LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  14Q LOSS MUTATED                4                  18
  14Q LOSS WILD-TYPE             58                 125
D67V17, multiclass
                                                 clus
vv                                                14Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                           18
                                                 clus
vv                                                14Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     34
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  58
  LIFELONG NON-SMOKER                                            125
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V18, continuous
D67V19, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    1  0
  14Q LOSS WILD-TYPE 24  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1    0
  14Q LOSS WILD-TYPE   24    3
                         clus
vv                        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   1                 24
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D67V20, continuous
D67V21, continuous
D67V22, continuous
D67V23, continuous
D67V24, continuous
D67V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  14Q LOSS MUTATED                                     0
  14Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  14Q LOSS MUTATED                                     1
  14Q LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  14Q LOSS MUTATED                         4                       0
  14Q LOSS WILD-TYPE                      32                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  14Q LOSS MUTATED                         1
  14Q LOSS WILD-TYPE                       7
D67V26, multiclass
                                     clus
vv                                    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                            4                 32
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  14Q LOSS MUTATED                                               0
  14Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  14Q LOSS MUTATED                                                1
  14Q LOSS WILD-TYPE                                             24
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  14Q LOSS MUTATED                                                                                  14
  14Q LOSS WILD-TYPE                                                                                68
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  14Q LOSS MUTATED                                                                                              7
  14Q LOSS WILD-TYPE                                                                                          114
D67V27, multiclass
                                                                                              clus
vv                                                                                             14Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                7
                                                                                              clus
vv                                                                                             14Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V28, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    7  8
  14Q LOSS WILD-TYPE 64 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      7    8
  14Q LOSS WILD-TYPE   64   66
         clus
vv        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ABSENT                 7                 64
  PRESENT                8                 66
[1] 2 2
[1] FALSE
D67V29, continuous
D67V30, continuous
D67V31, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     4  16
  14Q LOSS WILD-TYPE  45 101
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4   16
  14Q LOSS WILD-TYPE   45  101
                                          clus
vv                                         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 45
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               16                101
[1] 2 2
[1] FALSE
D67V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  14Q LOSS MUTATED              0           6          3
  14Q LOSS WILD-TYPE           15          48         82
D67V33, multiclass
              clus
vv             14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CURRENT USER                0                 15
  FORMER USER                 6                 48
  NEVER USED                  3                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V34, continuous
D67V35, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    9  2
  14Q LOSS WILD-TYPE 83 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      9    2
  14Q LOSS WILD-TYPE   83   16
         clus
vv        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ABSENT                 9                 83
  PRESENT                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  14Q LOSS MUTATED             0         9     1
  14Q LOSS WILD-TYPE           5        91     1
D67V36, multiclass
             clus
vv            14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                  9                 91
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V37, continuous
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GH-A9DA         TCGA-HM-A3JK         TCGA-JW-A852 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-JX-A3Q8         TCGA-MA-AA3W         TCGA-MA-AA3Z 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ZX-AA5X 
"14Q LOSS WILD-TYPE" 
D67V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  14Q LOSS MUTATED         0        0         0         0        3        12
  14Q LOSS WILD-TYPE       5        1         1         1       31        65
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  14Q LOSS MUTATED           6        1         0          1          0
  14Q LOSS WILD-TYPE        31        3         8          4          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  14Q LOSS MUTATED           3         0          0          4         1
  14Q LOSS WILD-TYPE        41         1          3         38         6
                    vv
clus                 STAGE IVB
  14Q LOSS MUTATED           1
  14Q LOSS WILD-TYPE        11
D67V39, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  3                 31
  STAGE IB1                12                 65
  STAGE IB2                 6                 31
  STAGE II                  1                  3
  STAGE IIA                 0                  8
  STAGE IIA1                1                  4
  STAGE IIA2                0                  7
  STAGE IIB                 3                 41
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB                4                 38
  STAGE IVA                 1                  6
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    31  13
  15Q LOSS WILD-TYPE 180  54
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                44                234 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                13                 54 
$`15Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1ML TCGA-C5-A2LV TCGA-C5-A7CG 
       57.04        35.01        38.99        20.91        73.45       210.67 
TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A8YQ TCGA-DG-A2KK TCGA-DR-A0ZL TCGA-DS-A7WH 
      154.32        17.19        23.51        82.06        87.75        17.52 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2PM TCGA-EK-A2RK TCGA-EK-A2RN 
       31.73        14.89        12.59         0.59         0.43         0.53 
TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3LH TCGA-JX-A3Q8 TCGA-LP-A4AX TCGA-MA-AA3X 
       21.67         9.44        78.71        44.61        12.49        19.56 
TCGA-MA-AA42 TCGA-MU-A8JM TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        8.52        19.96        17.23         2.96        15.58        16.41 
TCGA-VS-A8EJ TCGA-VS-A8QH TCGA-VS-A94Z TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A9U5 
       19.96        39.78        33.37        15.68        55.50        50.47 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UT TCGA-VS-A9UV TCGA-VS-A9UZ 
       24.30        46.92        45.11        15.85         3.42        67.20 
TCGA-VS-A9V4 TCGA-ZJ-A8QR 
        4.34        19.13 

$`15Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       57.73        53.16        35.61         0.46         2.43        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
        3.58        44.22        73.18        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE 
      101.82       134.33        15.48        20.35       147.35       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      131.11        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83         8.35       146.86        99.91        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91        14.73         1.12        95.11        44.94        63.98 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76        55.63        69.96        95.67        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18         8.28        39.55        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        26.01         0.30        24.82         7.46 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.48         0.36        60.72        26.27         6.64         1.51 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
       19.27         0.39         0.43         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK 
       40.96         4.31         0.10        47.77         0.10         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.76         0.03        20.35         7.92        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       19.79         8.32        15.55         1.22        23.84        19.04 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
       16.11        31.36        36.26        20.98        26.14         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
       16.14        28.31        14.01        35.44        10.55         1.12 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 
       17.75        25.41        16.57        20.78        14.93       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK 
      137.16        66.81       129.37        96.95        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        28.37         8.28        18.15        21.11       209.59 
TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU 
       20.91        11.28         0.89         0.30         0.82        13.35 
TCGA-MA-AA3W TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA43 TCGA-MU-A51Y 
       22.52        17.82        19.56         8.35        11.38        28.08 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       34.62        54.81        35.05        20.84        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       22.62        19.59        14.60        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       69.50        10.03        46.52        45.57        32.42        23.97 
TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       65.49        32.15        53.59        36.13        11.51        59.18 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A952 
       31.27        40.87        16.64         4.73        40.14        58.45 
TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       56.35        50.14        51.32        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       29.95        27.12         1.71        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UY TCGA-VS-A9V0 
       47.47        41.52        26.07        14.53        18.25        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 
        5.16        18.25        17.75        16.24        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26        67.59         0.69         1.41         0.16         3.91 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.43               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            210.67             209.59 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            20.435             23.905 
[1] "0.4 - 210.7 (20.4)" "0.0 - 209.6 (23.9)"
[1] "hr=" "1.3"
D68V2, continuous
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED    18  10   4   4
  15Q LOSS WILD-TYPE 117  60  17   4
D68V3, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               18                117
  T2               10                 60
  T3                4                 17
  T4                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V4, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20   6
  15Q LOSS WILD-TYPE 109  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20    6
  15Q LOSS WILD-TYPE  109   50
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               20                109
  1                6                 50
[1] 2 2
[1] FALSE
D68V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   12  3
  15Q LOSS WILD-TYPE 96  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     12    3
  15Q LOSS WILD-TYPE   96    7
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               12                 96
  1                3                  7
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     7  23
  15Q LOSS WILD-TYPE  48 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7   23
  15Q LOSS WILD-TYPE   48  100
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 7                 48
  YES               23                100
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED               1                               37
  15Q LOSS WILD-TYPE             5                              205
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  15Q LOSS MUTATED                                               0
  15Q LOSS WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  15Q LOSS MUTATED                                     2
  15Q LOSS WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  15Q LOSS MUTATED                                           1
  15Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  15Q LOSS MUTATED                                              6
  15Q LOSS WILD-TYPE                                           11
D68V7, multiclass
                                               clus
vv                                              15Q LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            37
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 6
                                               clus
vv                                              15Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             205
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, continuous
D68V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     5
  15Q LOSS WILD-TYPE                                8    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED                           9
  15Q LOSS WILD-TYPE                        19
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           1    27
  15Q LOSS WILD-TYPE                                         1   175
D68V10, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                                9                 19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  1
  WHITE                                                   27                175
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2  24
  15Q LOSS WILD-TYPE  21 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   24
  15Q LOSS WILD-TYPE   21  138
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 21
  NOT HISPANIC OR LATINO               24                138
[1] 2 2
[1] FALSE
D68V12, continuous
D68V13, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    28  13
  15Q LOSS WILD-TYPE 155  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     28   13
  15Q LOSS WILD-TYPE  155   61
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  TUMOR FREE               28                155
  WITH TUMOR               13                 61
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  15Q LOSS MUTATED     0  15  25   1   5
  15Q LOSS WILD-TYPE  18 114  90   0  19
D68V14, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  G1                0                 18
  G2               15                114
  G3               25                 90
  G4                1                  0
  GX                5                 19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V15, continuous
D68V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  15Q LOSS MUTATED                                             5
  15Q LOSS WILD-TYPE                                          33
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  15Q LOSS MUTATED                                        1
  15Q LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  15Q LOSS MUTATED                                                 1
  15Q LOSS WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  15Q LOSS MUTATED                8                  22
  15Q LOSS WILD-TYPE             54                 121
D68V17, multiclass
                                                 clus
vv                                                15Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 8
  LIFELONG NON-SMOKER                                           22
                                                 clus
vv                                                15Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  54
  LIFELONG NON-SMOKER                                            121
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V18, continuous
D68V19, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    4  0
  15Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    0
  15Q LOSS WILD-TYPE   21    3
                         clus
vv                        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D68V20, continuous
D68V21, continuous
D68V22, continuous
D68V23, continuous
D68V24, continuous
D68V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  15Q LOSS MUTATED                                     0
  15Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  15Q LOSS MUTATED                                     1
  15Q LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  15Q LOSS MUTATED                         7                       0
  15Q LOSS WILD-TYPE                      29                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  15Q LOSS MUTATED                         1
  15Q LOSS WILD-TYPE                       7
D68V26, multiclass
                                     clus
vv                                    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                            7                 29
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  15Q LOSS MUTATED                                               0
  15Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  15Q LOSS MUTATED                                                3
  15Q LOSS WILD-TYPE                                             22
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  15Q LOSS MUTATED                                                                                  21
  15Q LOSS WILD-TYPE                                                                                61
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  15Q LOSS MUTATED                                                                                             15
  15Q LOSS WILD-TYPE                                                                                          106
D68V27, multiclass
                                                                                              clus
vv                                                                                             15Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               15
                                                                                              clus
vv                                                                                             15Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            61
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V28, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    8  7
  15Q LOSS WILD-TYPE 63 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8    7
  15Q LOSS WILD-TYPE   63   67
         clus
vv        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ABSENT                 8                 63
  PRESENT                7                 67
[1] 2 2
[1] FALSE
D68V29, continuous
D68V30, continuous
D68V31, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    7 18
  15Q LOSS WILD-TYPE 42 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7   18
  15Q LOSS WILD-TYPE   42   99
                                          clus
vv                                         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    7                 42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               18                 99
[1] 2 2
[1] FALSE
D68V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  15Q LOSS MUTATED              1           8         14
  15Q LOSS WILD-TYPE           14          46         71
D68V33, multiclass
              clus
vv             15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 8                 46
  NEVER USED                 14                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V34, continuous
D68V35, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    8  1
  15Q LOSS WILD-TYPE 84 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8    1
  15Q LOSS WILD-TYPE   84   17
         clus
vv        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ABSENT                 8                 84
  PRESENT                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  15Q LOSS MUTATED             0        18     1
  15Q LOSS WILD-TYPE           5        82     1
D68V36, multiclass
             clus
vv            15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 18                 82
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V37, continuous
D68V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  15Q LOSS MUTATED         1        0         0         1        6        13
  15Q LOSS WILD-TYPE       4        1         1         0       28        64
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  15Q LOSS MUTATED           2        0         1          2          0
  15Q LOSS WILD-TYPE        35        4         7          3          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  15Q LOSS MUTATED           8         0          1          5         4
  15Q LOSS WILD-TYPE        36         1          2         37         3
                    vv
clus                 STAGE IVB
  15Q LOSS MUTATED           1
  15Q LOSS WILD-TYPE        11
D68V39, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  6                 28
  STAGE IB1                13                 64
  STAGE IB2                 2                 35
  STAGE II                  0                  4
  STAGE IIA                 1                  7
  STAGE IIA1                2                  3
  STAGE IIA2                0                  7
  STAGE IIB                 8                 36
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                5                 37
  STAGE IVA                 4                  3
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    19  10
  16P LOSS WILD-TYPE 192  57
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                29                249 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                 57 
$`16P LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1ML 
       23.67       173.29        35.01        57.73         0.46        20.91 
TCGA-C5-A2LT TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-C5-A8XH 
       73.18        18.02       210.67        17.19        13.61        45.83 
TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PM TCGA-FU-A3TX TCGA-HM-A6W2 
       26.01         1.51        19.27         0.59         1.48         9.44 
TCGA-IR-A3LB TCGA-IR-A3LF TCGA-JX-A5QV TCGA-LP-A7HU TCGA-MA-AA43 TCGA-VS-A8EB 
       66.81        96.95        20.91        13.35        11.38        10.03 
TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A9UD TCGA-VS-A9V4 TCGA-WL-A834 
       46.52        19.96        24.30         4.34        26.01 

$`16P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN 
       18.74        36.56       144.16       177.04        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF 
       19.86        67.46        31.40        46.32        30.21        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99        35.61         2.43        40.93         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.45        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       52.01        17.85        20.42       154.32       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48        20.35       147.35       155.77       131.11        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK 
        9.34         2.73        50.99         8.35       146.86        99.91 
TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH 
       23.51        27.52        20.81        20.91        14.73         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM 
       95.11        82.06        44.94        63.98        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76        55.63        69.96        95.67        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18        17.52         8.28        39.55        40.87        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        31.73         0.30        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        25.91        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       24.00        13.48         0.36        12.59        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 
        6.64         0.39         0.43         0.36         1.45         0.13 
TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN 
       40.96         4.31         0.10         0.43        47.77         0.53 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.10         0.49         0.76         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K 
       15.22        14.70        19.79         8.32        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
       26.14        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.12        17.75        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI 
       14.93       147.39       137.16       129.37        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ 
       29.85        36.36        27.42         3.29        24.56        21.44 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       20.48        15.58        28.37         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 
      209.59        44.61        11.28         0.89        12.49         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
        0.82        22.52        19.56        17.82        19.56         8.35 
TCGA-MA-AA42 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        8.52        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       20.84        17.23         2.96        15.58        16.41        15.95 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q 
        9.04        16.14        17.56        14.07        15.88         9.34 
TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       18.64        22.62        19.59        14.60        11.67        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL 
       12.16        69.50        45.57        32.42        23.97        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        53.59        36.13        11.51        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 
       31.27        40.87        16.64         4.73        33.37        40.14 
TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 
       58.45        15.68        56.35        55.50        50.14        51.32 
TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       50.47        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO 
       46.92        45.11         1.71        14.53        27.25        47.87 
TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.47        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
       18.25        67.20        18.84         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       16.24        15.42        29.26        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.46               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            210.67             209.59 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             20.91              23.84 
[1] "0.5 - 210.7 (20.9)" "0.0 - 209.6 (23.8)"
[1] "hr=" "1.5"
D69V2, continuous
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED    17   3   5   1
  16P LOSS WILD-TYPE 118  67  16   7
D69V3, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               17                118
  T2                3                 67
  T3                5                 16
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V4, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    18   2
  16P LOSS WILD-TYPE 111  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     18    2
  16P LOSS WILD-TYPE  111   54
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               18                111
  1                2                 54
[1] 2 2
[1] FALSE
D69V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   15  3
  16P LOSS WILD-TYPE 93  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     15    3
  16P LOSS WILD-TYPE   93    7
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               15                 93
  1                3                  7
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7  12
  16P LOSS WILD-TYPE  48 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7   12
  16P LOSS WILD-TYPE   48  111
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 7                 48
  YES               12                111
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED               1                               25
  16P LOSS WILD-TYPE             5                              217
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16P LOSS MUTATED                                               2
  16P LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16P LOSS MUTATED                                     5
  16P LOSS WILD-TYPE                                  16
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16P LOSS MUTATED                                           0
  16P LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16P LOSS MUTATED                                              1
  16P LOSS WILD-TYPE                                           16
D69V7, multiclass
                                               clus
vv                                              16P LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            25
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              16P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             217
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, continuous
D69V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     2
  16P LOSS WILD-TYPE                                8    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED                           3
  16P LOSS WILD-TYPE                        25
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           0    27
  16P LOSS WILD-TYPE                                         2   175
D69V10, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                3                 25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   27                175
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1  19
  16P LOSS WILD-TYPE  22 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   19
  16P LOSS WILD-TYPE   22  143
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 22
  NOT HISPANIC OR LATINO               19                143
[1] 2 2
[1] FALSE
D69V12, continuous
D69V13, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    18  10
  16P LOSS WILD-TYPE 165  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     18   10
  16P LOSS WILD-TYPE  165   64
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  TUMOR FREE               18                165
  WITH TUMOR               10                 64
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  16P LOSS MUTATED     1  10  20   0   1
  16P LOSS WILD-TYPE  17 119  95   1  23
D69V14, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  G1                1                 17
  G2               10                119
  G3               20                 95
  G4                0                  1
  GX                1                 23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V15, continuous
D69V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16P LOSS MUTATED                                             7
  16P LOSS WILD-TYPE                                          31
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  16P LOSS MUTATED                                        1
  16P LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  16P LOSS MUTATED                                                 0
  16P LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16P LOSS MUTATED                4                  12
  16P LOSS WILD-TYPE             58                 131
D69V17, multiclass
                                                 clus
vv                                                16P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                           12
                                                 clus
vv                                                16P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  58
  LIFELONG NON-SMOKER                                            131
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V18, continuous
D69V19, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    4  0
  16P LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    0
  16P LOSS WILD-TYPE   21    3
                         clus
vv                        16P LOSS MUTATED 16P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D69V20, continuous
D69V21, continuous
D69V22, continuous
D69V23, continuous
D69V24, continuous
D69V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  16P LOSS MUTATED                                     0
  16P LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  16P LOSS MUTATED                                     2
  16P LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  16P LOSS MUTATED                         8                       0
  16P LOSS WILD-TYPE                      28                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16P LOSS MUTATED                         0
  16P LOSS WILD-TYPE                       8
D69V26, multiclass
                                     clus
vv                                    16P LOSS MUTATED 16P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  5
  OTHER LOCATION, SPECIFY                            8                 28
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  16P LOSS MUTATED                                               0
  16P LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  16P LOSS MUTATED                                                2
  16P LOSS WILD-TYPE                                             23
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16P LOSS MUTATED                                                                                  11
  16P LOSS WILD-TYPE                                                                                71
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16P LOSS MUTATED                                                                                              9
  16P LOSS WILD-TYPE                                                                                          112
D69V27, multiclass
                                                                                              clus
vv                                                                                             16P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          11
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                9
                                                                                              clus
vv                                                                                             16P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            71
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V28, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    6  9
  16P LOSS WILD-TYPE 65 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      6    9
  16P LOSS WILD-TYPE   65   65
         clus
vv        16P LOSS MUTATED 16P LOSS WILD-TYPE
  ABSENT                 6                 65
  PRESENT                9                 65
[1] 2 2
[1] FALSE
D69V29, continuous
D69V30, continuous
D69V31, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     9   8
  16P LOSS WILD-TYPE  40 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      9    8
  16P LOSS WILD-TYPE   40  109
                                          clus
vv                                         16P LOSS MUTATED 16P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                8                109
[1] 2 2
[1] FALSE
D69V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16P LOSS MUTATED              1           5         10
  16P LOSS WILD-TYPE           14          49         75
D69V33, multiclass
              clus
vv             16P LOSS MUTATED 16P LOSS WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 5                 49
  NEVER USED                 10                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V34, continuous
D69V35, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    9  1
  16P LOSS WILD-TYPE 83 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      9    1
  16P LOSS WILD-TYPE   83   17
         clus
vv        16P LOSS MUTATED 16P LOSS WILD-TYPE
  ABSENT                 9                 83
  PRESENT                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  16P LOSS MUTATED             1         9     0
  16P LOSS WILD-TYPE           4        91     2
D69V36, multiclass
             clus
vv            16P LOSS MUTATED 16P LOSS WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                  9                 91
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V37, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MA-AA3W         TCGA-MA-AA3Z         TCGA-MA-AA42 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ZX-AA5X 
"16P LOSS WILD-TYPE" 
D69V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  16P LOSS MUTATED         0        0         0         0        6         9
  16P LOSS WILD-TYPE       5        1         1         1       28        68
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  16P LOSS MUTATED           5        1         0          0          0
  16P LOSS WILD-TYPE        32        3         8          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  16P LOSS MUTATED           2         0          1          4         1
  16P LOSS WILD-TYPE        42         1          2         38         6
                    vv
clus                 STAGE IVB
  16P LOSS MUTATED           2
  16P LOSS WILD-TYPE        10
D69V39, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  6                 28
  STAGE IB1                 9                 68
  STAGE IB2                 5                 32
  STAGE II                  1                  3
  STAGE IIA                 0                  8
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 2                 42
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                4                 38
  STAGE IVA                 1                  6
  STAGE IVB                 2                 10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    30  10
  16Q LOSS WILD-TYPE 181  57
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                40                238 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 57 
$`16Q LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1ML 
       23.67       173.29        35.01        57.73         0.46        20.91 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CG 
       44.22        73.18        83.05        38.43        18.02       210.67 
TCGA-C5-A7CO TCGA-C5-A8XH TCGA-DS-A7WH TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2PI 
      147.35        45.83        17.52        26.01         1.51        19.27 
TCGA-EK-A2PM TCGA-EK-A3GM TCGA-EX-A1H6 TCGA-EX-A8YF TCGA-FU-A3TX TCGA-FU-A770 
        0.59         0.76         7.92        15.55         1.48         1.12 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-JX-A5QV TCGA-LP-A7HU TCGA-MA-AA43 
      137.16        66.81        96.95        20.91        13.35        11.38 
TCGA-MY-A5BF TCGA-VS-A8EC TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A9UD TCGA-VS-A9UO 
       20.84        46.52        19.96        32.15        24.30        47.87 
TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.25        18.84         4.34        16.24 

$`16Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN 
       18.74        36.56       144.16       177.04        82.85         5.46 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF 
       19.86        67.46        31.40        46.32        30.21        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LV 
       38.99        35.61         2.43        40.93         3.58        73.45 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35       100.14        33.24        52.01        17.85        20.42 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC 
      154.32       101.82       134.33        15.48        20.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
      155.77       131.11        94.95         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99         8.35       146.86        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       20.81        20.91        14.73         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI 
       69.96        95.67        22.98        16.83        16.18         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       39.55        40.87        37.35        30.90        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05        25.02        36.89        26.40        24.56        31.73 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        0.30        24.82         7.46        14.89        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       27.29        27.25        27.22        24.00        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PK TCGA-EK-A2PL 
       12.59        60.72        26.27         6.64         0.39         0.43 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.36         1.45         0.13        40.96         4.31         0.10 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        0.43        47.77         0.53         0.10         0.49         0.03 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
       20.35        15.22        14.70        19.79         8.32         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
       26.14        16.14        28.31        14.01        35.44        10.55 
TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
       17.75        25.41        16.57        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
        9.44       147.39       129.37        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        28.37         8.28        18.15        21.11       209.59 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       44.61        11.28         0.89        12.49         0.30         0.82 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 
       22.52        19.56        17.82        19.56         8.35         8.52 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 
       28.08        34.62        19.96        54.81        35.05        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI 
       19.59        14.60        11.67        93.99        12.16        69.50 
TCGA-VS-A8EB TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q9 
       10.03        45.57        32.42        23.97        65.49        53.59 
TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       36.13        11.51        59.18        39.78        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 
       16.64         4.73        33.37        40.14        58.45        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       56.35        55.50        50.14        51.32        50.47        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UI 
       48.39        28.50        29.95        27.12        46.92        45.11 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
        1.71        14.53        27.25        47.47        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 
       15.85        14.53         3.42        67.20         5.16        18.25 
TCGA-VS-A9V3 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       17.75        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.46               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            210.67             209.59 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            20.910             23.675 
[1] "0.5 - 210.7 (20.9)" "0.0 - 209.6 (23.7)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED    23   8   4   1
  16Q LOSS WILD-TYPE 112  62  17   7
D70V3, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               23                112
  T2                8                 62
  T3                4                 17
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V4, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    25   3
  16Q LOSS WILD-TYPE 104  53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     25    3
  16Q LOSS WILD-TYPE  104   53
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               25                104
  1                3                 53
[1] 2 2
[1] FALSE
D70V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   17  1
  16Q LOSS WILD-TYPE 91  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     17    1
  16Q LOSS WILD-TYPE   91    9
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               17                 91
  1                1                  9
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     9  18
  16Q LOSS WILD-TYPE  46 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      9   18
  16Q LOSS WILD-TYPE   46  105
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 9                 46
  YES               18                105
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED               0                               26
  16Q LOSS WILD-TYPE             6                              216
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16Q LOSS MUTATED                                               4
  16Q LOSS WILD-TYPE                                             2
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16Q LOSS MUTATED                                     8
  16Q LOSS WILD-TYPE                                  13
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16Q LOSS MUTATED                                           1
  16Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16Q LOSS MUTATED                                              5
  16Q LOSS WILD-TYPE                                           12
D70V7, multiclass
                                               clus
vv                                              16Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            26
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 5
                                               clus
vv                                              16Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             216
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, continuous
D70V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     2
  16Q LOSS WILD-TYPE                                8    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED                           1
  16Q LOSS WILD-TYPE                        27
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           0    37
  16Q LOSS WILD-TYPE                                         2   165
D70V10, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                1                 27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   37                165
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     2  22
  16Q LOSS WILD-TYPE  21 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2   22
  16Q LOSS WILD-TYPE   21  140
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 21
  NOT HISPANIC OR LATINO               22                140
[1] 2 2
[1] FALSE
D70V12, continuous
D70V13, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    25  12
  16Q LOSS WILD-TYPE 158  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     25   12
  16Q LOSS WILD-TYPE  158   62
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  TUMOR FREE               25                158
  WITH TUMOR               12                 62
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  16Q LOSS MUTATED     4  20  18   0   0
  16Q LOSS WILD-TYPE  14 109  97   1  24
D70V14, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  G1                4                 14
  G2               20                109
  G3               18                 97
  G4                0                  1
  GX                0                 24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V15, continuous
D70V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16Q LOSS MUTATED                                             7
  16Q LOSS WILD-TYPE                                          31
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  16Q LOSS MUTATED                                        2
  16Q LOSS WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  16Q LOSS MUTATED                                                 0
  16Q LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16Q LOSS MUTATED                5                  23
  16Q LOSS WILD-TYPE             57                 120
D70V17, multiclass
                                                 clus
vv                                                16Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 5
  LIFELONG NON-SMOKER                                           23
                                                 clus
vv                                                16Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  57
  LIFELONG NON-SMOKER                                            120
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V18, continuous
D70V19, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    5  0
  16Q LOSS WILD-TYPE 20  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5    0
  16Q LOSS WILD-TYPE   20    3
                         clus
vv                        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   5                 20
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D70V20, continuous
D70V21, continuous
D70V22, continuous
D70V23, continuous
D70V24, continuous
D70V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  16Q LOSS MUTATED                                     0
  16Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  16Q LOSS MUTATED                                     1
  16Q LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  16Q LOSS MUTATED                         9                       0
  16Q LOSS WILD-TYPE                      27                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16Q LOSS MUTATED                         1
  16Q LOSS WILD-TYPE                       7
D70V26, multiclass
                                     clus
vv                                    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                            9                 27
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  16Q LOSS MUTATED                                               0
  16Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  16Q LOSS MUTATED                                                3
  16Q LOSS WILD-TYPE                                             22
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16Q LOSS MUTATED                                                                                  16
  16Q LOSS WILD-TYPE                                                                                66
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16Q LOSS MUTATED                                                                                             14
  16Q LOSS WILD-TYPE                                                                                          107
D70V27, multiclass
                                                                                              clus
vv                                                                                             16Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               14
                                                                                              clus
vv                                                                                             16Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            66
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V28, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   11 10
  16Q LOSS WILD-TYPE 60 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     11   10
  16Q LOSS WILD-TYPE   60   64
         clus
vv        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ABSENT                11                 60
  PRESENT               10                 64
[1] 2 2
[1] FALSE
D70V29, continuous
D70V30, continuous
D70V31, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     9   9
  16Q LOSS WILD-TYPE  40 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      9    9
  16Q LOSS WILD-TYPE   40  108
                                          clus
vv                                         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                9                108
[1] 2 2
[1] FALSE
D70V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16Q LOSS MUTATED              2           8         13
  16Q LOSS WILD-TYPE           13          46         72
D70V33, multiclass
              clus
vv             16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CURRENT USER                2                 13
  FORMER USER                 8                 46
  NEVER USED                 13                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V34, continuous
D70V35, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   15  1
  16Q LOSS WILD-TYPE 77 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     15    1
  16Q LOSS WILD-TYPE   77   17
         clus
vv        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ABSENT                15                 77
  PRESENT                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  16Q LOSS MUTATED             1        14     0
  16Q LOSS WILD-TYPE           4        86     2
D70V36, multiclass
             clus
vv            16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 14                 86
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V37, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 16 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-EK-A2RO         TCGA-GH-A9DA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-MA-AA3W         TCGA-MA-AA3Z         TCGA-MA-AA42 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-MY-A913 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ZX-AA5X 
"16Q LOSS WILD-TYPE" 
D70V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  16Q LOSS MUTATED         0        0         0         0        6        15
  16Q LOSS WILD-TYPE       5        1         1         1       28        62
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  16Q LOSS MUTATED           7        1         1          0          1
  16Q LOSS WILD-TYPE        30        3         7          5          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  16Q LOSS MUTATED           4         0          1          4         1
  16Q LOSS WILD-TYPE        40         1          2         38         6
                    vv
clus                 STAGE IVB
  16Q LOSS MUTATED           1
  16Q LOSS WILD-TYPE        11
D70V39, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  6                 28
  STAGE IB1                15                 62
  STAGE IB2                 7                 30
  STAGE II                  1                  3
  STAGE IIA                 1                  7
  STAGE IIA1                0                  5
  STAGE IIA2                1                  6
  STAGE IIB                 4                 40
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                4                 38
  STAGE IVA                 1                  6
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    66  26
  17P LOSS WILD-TYPE 145  41
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                92                186 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                26                 41 
$`17P LOSS MUTATED`
TCGA-4J-AA1J TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ 
       17.82        68.84       144.16       173.29         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2M1 
       67.46        38.99        40.93        73.18        83.05        38.43 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       15.48       147.35        17.19         9.34        13.61         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8ZZ TCGA-DG-A2KJ 
       50.99        45.83       146.86        23.51        20.91        95.11 
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A439 
       87.75        36.76        55.63        95.67        40.87        31.73 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       26.01         0.30        27.25        27.22        24.00        13.48 
TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
        0.36        60.72         1.51         1.45         0.13        40.96 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GM TCGA-EX-A1H5 
        0.10         0.43         0.53         0.10         0.76        20.35 
TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A3NI TCGA-GH-A9DA TCGA-IR-A3LH TCGA-IR-A3LK 
       15.22         8.32        20.98        17.75        78.71        29.85 
TCGA-JW-A5VI TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MA-AA3X TCGA-MA-AA3Y 
       24.56        28.37        11.28         0.89        19.56        17.82 
TCGA-MU-A5YI TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73Q TCGA-Q1-A73S 
       34.62         2.96        16.41         9.04         9.34        22.62 
TCGA-RA-A741 TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EI TCGA-VS-A8QC 
       14.60        12.16        69.50        10.03        23.97        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A957 
       59.18        39.78         4.73        40.14        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9UI TCGA-VS-A9UP TCGA-VS-A9UR 
       50.14        51.32        43.40        45.11        47.47        26.07 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V3 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
        3.42        18.25        17.75        67.59        19.13         0.69 
TCGA-ZJ-AAXA TCGA-ZX-AA5X 
        1.41         3.91 

$`17P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF 
       17.52        49.48        57.04        23.67        11.44        18.74 
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
       36.56       177.04        82.85        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       35.01        57.73        53.16        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ 
       20.91         3.58        44.22        73.45        78.35       100.14 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7UE TCGA-C5-A7UH 
      154.32       101.82       134.33        20.35       155.77       131.11 
TCGA-C5-A7UI TCGA-C5-A8XI TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A907 
       94.95         8.35        99.91        27.52        20.81        14.73 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VM 
        1.12        82.06        44.94        63.98        58.88        69.96 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       36.89        26.40        24.56        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP 
       26.79        25.91        27.29        12.59        26.27         6.64 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2RC 
       19.27         0.39         0.43         0.59         0.36         4.31 
TCGA-EK-A2RL TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L 
       47.77         0.49         0.03         7.92        14.70        19.79 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       15.55         1.22        23.84        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       36.26        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44        10.55         1.12        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
      129.37        96.95        81.96        36.36        27.42         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       21.44        20.48        15.58         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
      209.59        44.61        20.91        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 
       13.35        22.52        19.56         8.35         8.52        11.38 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       28.08        19.96        54.81        35.05        20.84        17.23 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.58        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EC TCGA-VS-A8EG 
       18.64        19.59        11.67        93.99        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       32.42        19.96        65.49        32.15        53.59        36.13 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 
       31.27        40.87        16.64        33.37        58.45        15.68 
TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD 
       50.47        48.39        28.50        29.95        27.12        24.30 
TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UQ 
       46.92         1.71        14.53        27.25        47.87        41.52 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 
       15.85        14.53        67.20        18.84         5.16        18.25 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-AAXU 
        4.34        16.24        15.42        26.01        29.26         0.16 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.10               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            173.29             210.67 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            23.065             23.325 
[1] "0.1 - 173.3 (23.1)" "0.0 - 210.7 (23.3)"
[1] "hr=" "1.3"
D71V2, continuous
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED   41 19  6  3
  17P LOSS WILD-TYPE 94 51 15  5
D71V3, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               41                 94
  T2               19                 51
  T3                6                 15
  T4                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V4, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   34 14
  17P LOSS WILD-TYPE 95 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     34   14
  17P LOSS WILD-TYPE   95   42
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               34                 95
  1               14                 42
[1] 2 2
[1] FALSE
D71V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   32  2
  17P LOSS WILD-TYPE 76  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     32    2
  17P LOSS WILD-TYPE   76    8
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               32                 76
  1                2                  8
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   20 43
  17P LOSS WILD-TYPE 35 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     20   43
  17P LOSS WILD-TYPE   35   80
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                20                 35
  YES               43                 80
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED               1                               85
  17P LOSS WILD-TYPE             5                              157
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17P LOSS MUTATED                                               1
  17P LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17P LOSS MUTATED                                     3
  17P LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17P LOSS MUTATED                                           1
  17P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17P LOSS MUTATED                                              4
  17P LOSS WILD-TYPE                                           13
D71V7, multiclass
                                               clus
vv                                              17P LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            85
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 4
                                               clus
vv                                              17P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             157
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, continuous
D71V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  2     8
  17P LOSS WILD-TYPE                                6    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED                           7
  17P LOSS WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           2    68
  17P LOSS WILD-TYPE                                         0   134
D71V10, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    8                 11
  BLACK OR AFRICAN AMERICAN                                7                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  0
  WHITE                                                   68                134
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     5  58
  17P LOSS WILD-TYPE  18 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5   58
  17P LOSS WILD-TYPE   18  104
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 18
  NOT HISPANIC OR LATINO               58                104
[1] 2 2
[1] FALSE
D71V12, continuous
D71V13, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    52  32
  17P LOSS WILD-TYPE 131  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     52   32
  17P LOSS WILD-TYPE  131   42
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  TUMOR FREE               52                131
  WITH TUMOR               32                 42
[1] 2 2
[1] FALSE
                    vv
clus                 G1 G2 G3 G4 GX
  17P LOSS MUTATED    3 38 38  1 13
  17P LOSS WILD-TYPE 15 91 77  0 11
D71V14, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  G1                3                 15
  G2               38                 91
  G3               38                 77
  G4                1                  0
  GX               13                 11
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V15, continuous
D71V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17P LOSS MUTATED                                            12
  17P LOSS WILD-TYPE                                          26
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  17P LOSS MUTATED                                        5
  17P LOSS WILD-TYPE                                      4
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  17P LOSS MUTATED                                                 0
  17P LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17P LOSS MUTATED               22                  42
  17P LOSS WILD-TYPE             40                 101
D71V17, multiclass
                                                 clus
vv                                                17P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                22
  LIFELONG NON-SMOKER                                           42
                                                 clus
vv                                                17P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     26
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  40
  LIFELONG NON-SMOKER                                            101
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V18, continuous
D71V19, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    9  1
  17P LOSS WILD-TYPE 16  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      9    1
  17P LOSS WILD-TYPE   16    2
                         clus
vv                        17P LOSS MUTATED 17P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D71V20, continuous
D71V21, continuous
D71V22, continuous
D71V23, continuous
D71V24, continuous
D71V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  17P LOSS MUTATED                                     0
  17P LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  17P LOSS MUTATED                                     2
  17P LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  17P LOSS MUTATED                        11                       0
  17P LOSS WILD-TYPE                      25                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17P LOSS MUTATED                         4
  17P LOSS WILD-TYPE                       4
D71V26, multiclass
                                     clus
vv                                    17P LOSS MUTATED 17P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  5
  OTHER LOCATION, SPECIFY                           11                 25
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            4                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  17P LOSS MUTATED                                               1
  17P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  17P LOSS MUTATED                                                7
  17P LOSS WILD-TYPE                                             18
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17P LOSS MUTATED                                                                                  28
  17P LOSS WILD-TYPE                                                                                54
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17P LOSS MUTATED                                                                                             38
  17P LOSS WILD-TYPE                                                                                           83
D71V27, multiclass
                                                                                              clus
vv                                                                                             17P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               38
                                                                                              clus
vv                                                                                             17P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            54
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V28, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   21 22
  17P LOSS WILD-TYPE 50 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     21   22
  17P LOSS WILD-TYPE   50   52
         clus
vv        17P LOSS MUTATED 17P LOSS WILD-TYPE
  ABSENT                21                 50
  PRESENT               22                 52
[1] 2 2
[1] FALSE
D71V29, continuous
D71V30, continuous
D71V31, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   21 40
  17P LOSS WILD-TYPE 28 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     21   40
  17P LOSS WILD-TYPE   28   77
                                          clus
vv                                         17P LOSS MUTATED 17P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   21                 28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               40                 77
[1] 2 2
[1] FALSE
D71V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17P LOSS MUTATED              3          13         30
  17P LOSS WILD-TYPE           12          41         55
D71V33, multiclass
              clus
vv             17P LOSS MUTATED 17P LOSS WILD-TYPE
  CURRENT USER                3                 12
  FORMER USER                13                 41
  NEVER USED                 30                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V34, continuous
D71V35, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   29  4
  17P LOSS WILD-TYPE 63 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     29    4
  17P LOSS WILD-TYPE   63   14
         clus
vv        17P LOSS MUTATED 17P LOSS WILD-TYPE
  ABSENT                29                 63
  PRESENT                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  17P LOSS MUTATED             1        37     1
  17P LOSS WILD-TYPE           4        63     1
D71V36, multiclass
             clus
vv            17P LOSS MUTATED 17P LOSS WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 37                 63
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V37, continuous
D71V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  17P LOSS MUTATED         3        1         1         1       11        22
  17P LOSS WILD-TYPE       2        0         0         0       23        55
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  17P LOSS MUTATED          11        1         3          3          1
  17P LOSS WILD-TYPE        26        3         5          2          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  17P LOSS MUTATED          14         0          1         14         2
  17P LOSS WILD-TYPE        30         1          2         28         5
                    vv
clus                 STAGE IVB
  17P LOSS MUTATED           4
  17P LOSS WILD-TYPE         8
D71V39, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                  1                  0
  STAGE IA1                 1                  0
  STAGE IA2                 1                  0
  STAGE IB                 11                 23
  STAGE IB1                22                 55
  STAGE IB2                11                 26
  STAGE II                  1                  3
  STAGE IIA                 3                  5
  STAGE IIA1                3                  2
  STAGE IIA2                1                  6
  STAGE IIB                14                 30
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB               14                 28
  STAGE IVA                 2                  5
  STAGE IVB                 4                  8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    25  11
  17Q LOSS WILD-TYPE 186  56
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                36                242 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                11                 56 
$`17Q LOSS MUTATED`
TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A7CO TCGA-C5-A7UC 
       38.99        40.93        73.18        83.05       147.35        17.19 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8YQ TCGA-DG-A2KJ TCGA-DS-A0VK 
      131.11         9.34         2.73        23.51        95.11        36.76 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A43B TCGA-EA-A97N TCGA-EK-A2PG TCGA-EK-A2R8 
       95.67        40.87        26.01         0.36         1.51         1.45 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EX-A69M TCGA-GH-A9DA TCGA-JW-A5VI 
        0.10         0.43         0.53         8.32        17.75        24.56 
TCGA-MA-AA3X TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8QC TCGA-VS-A8QH TCGA-VS-A950 
       19.56        12.16        69.50        11.51        39.78        40.14 
TCGA-VS-A954 TCGA-VS-A9UI TCGA-VS-A9UP TCGA-VS-A9V3 TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
       56.35        45.11        47.47        17.75         0.69         1.41 

$`17Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ 
       30.21        35.01        57.73        53.16        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY 
        2.43        20.91         3.58        44.22        73.45        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH 
       20.35       155.77        94.95        13.61        50.99        45.83 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ 
        8.35       146.86        99.91        27.52        20.81        20.91 
TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
       14.73         1.12        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       58.88        55.63        69.96        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       17.52         8.28        39.55        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       31.73         0.30        24.82         7.46        14.89        26.79 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       25.91        27.29        27.25        27.22        24.00        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PK 
       12.59        60.72        26.27         6.64        19.27         0.39 
TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC 
        0.43         0.59         0.36         0.13        40.96         4.31 
TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 
       47.77         0.10         0.49         0.76         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K 
        7.92        15.22        14.70        19.79        15.55         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84        19.04        16.11        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
       26.14         1.48        16.14        28.31        14.01        35.44 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
       10.55         1.12        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         9.44       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       18.15        21.11       209.59        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W 
        0.89        12.49         0.30         0.82        13.35        22.52 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         8.35         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       34.62        19.96        54.81        35.05        20.84        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-VS-A8EB TCGA-VS-A8EC 
       19.59        14.60        11.67        93.99        10.03        46.52 
TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 
       45.57        32.42        23.97        19.96        65.49        32.15 
TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       53.59        36.13        59.18        31.27        40.87        16.64 
TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A957 TCGA-VS-A958 
        4.73        33.37        58.45        15.68        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       51.32        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       27.12        24.30        46.92         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV 
       47.87        41.52        26.07        15.85        14.53         3.42 
TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V4 
       18.25        67.20        18.84         5.16        18.25         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.16         3.91 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            147.35             210.67 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            24.035             22.800 
[1] "0.1 - 147.3 (24.0)" "0.0 - 210.7 (22.8)"
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED    16   7   4   1
  17Q LOSS WILD-TYPE 119  63  17   7
D72V3, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               16                119
  T2                7                 63
  T3                4                 17
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V4, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    14   7
  17Q LOSS WILD-TYPE 115  49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     14    7
  17Q LOSS WILD-TYPE  115   49
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               14                115
  1                7                 49
[1] 2 2
[1] FALSE
D72V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   11  0
  17Q LOSS WILD-TYPE 97 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     11    0
  17Q LOSS WILD-TYPE   97   10
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               11                 97
  1                0                 10
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     7  17
  17Q LOSS WILD-TYPE  48 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   17
  17Q LOSS WILD-TYPE   48  106
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 7                 48
  YES               17                106
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED               0                               33
  17Q LOSS WILD-TYPE             6                              209
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17Q LOSS MUTATED                                               0
  17Q LOSS WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17Q LOSS MUTATED                                     0
  17Q LOSS WILD-TYPE                                  21
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17Q LOSS MUTATED                                           1
  17Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17Q LOSS MUTATED                                              3
  17Q LOSS WILD-TYPE                                           14
D72V7, multiclass
                                               clus
vv                                              17Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            33
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 3
                                               clus
vv                                              17Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             209
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  14
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V8, continuous
D72V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  2     0
  17Q LOSS WILD-TYPE                                6    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED                           2
  17Q LOSS WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           0    29
  17Q LOSS WILD-TYPE                                         2   173
D72V10, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                2                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   29                173
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  23
  17Q LOSS WILD-TYPE  22 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   23
  17Q LOSS WILD-TYPE   22  139
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 22
  NOT HISPANIC OR LATINO               23                139
[1] 2 2
[1] FALSE
D72V12, continuous
D72V13, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    19  11
  17Q LOSS WILD-TYPE 164  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     19   11
  17Q LOSS WILD-TYPE  164   63
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  TUMOR FREE               19                164
  WITH TUMOR               11                 63
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  17Q LOSS MUTATED     2  17  17   0   1
  17Q LOSS WILD-TYPE  16 112  98   1  23
D72V14, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  G1                2                 16
  G2               17                112
  G3               17                 98
  G4                0                  1
  GX                1                 23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, continuous
D72V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17Q LOSS MUTATED                                             3
  17Q LOSS WILD-TYPE                                          35
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  17Q LOSS MUTATED                                        3
  17Q LOSS WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  17Q LOSS MUTATED                                                 0
  17Q LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17Q LOSS MUTATED               11                  12
  17Q LOSS WILD-TYPE             51                 131
D72V17, multiclass
                                                 clus
vv                                                17Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                11
  LIFELONG NON-SMOKER                                           12
                                                 clus
vv                                                17Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     35
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  51
  LIFELONG NON-SMOKER                                            131
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V18, continuous
D72V19, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  0
  17Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE   21    3
                         clus
vv                        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D72V20, continuous
D72V21, continuous
D72V22, continuous
D72V23, continuous
D72V24, continuous
D72V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  17Q LOSS MUTATED                                     0
  17Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  17Q LOSS MUTATED                                     0
  17Q LOSS WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  17Q LOSS MUTATED                         5                       0
  17Q LOSS WILD-TYPE                      31                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17Q LOSS MUTATED                         3
  17Q LOSS WILD-TYPE                       5
D72V26, multiclass
                                     clus
vv                                    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            5                 31
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  17Q LOSS MUTATED                                               0
  17Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  17Q LOSS MUTATED                                                2
  17Q LOSS WILD-TYPE                                             23
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17Q LOSS MUTATED                                                                                  14
  17Q LOSS WILD-TYPE                                                                                68
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17Q LOSS MUTATED                                                                                             11
  17Q LOSS WILD-TYPE                                                                                          110
D72V27, multiclass
                                                                                              clus
vv                                                                                             17Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               11
                                                                                              clus
vv                                                                                             17Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V28, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    9  7
  17Q LOSS WILD-TYPE 62 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9    7
  17Q LOSS WILD-TYPE   62   67
         clus
vv        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ABSENT                 9                 62
  PRESENT                7                 67
[1] 2 2
[1] FALSE
D72V29, continuous
D72V30, continuous
D72V31, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     9  15
  17Q LOSS WILD-TYPE  40 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9   15
  17Q LOSS WILD-TYPE   40  102
                                          clus
vv                                         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               15                102
[1] 2 2
[1] FALSE
D72V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17Q LOSS MUTATED              1           7         11
  17Q LOSS WILD-TYPE           14          47         74
D72V33, multiclass
              clus
vv             17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 7                 47
  NEVER USED                 11                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V34, continuous
D72V35, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   10  0
  17Q LOSS WILD-TYPE 82 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    0
  17Q LOSS WILD-TYPE   82   18
         clus
vv        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ABSENT                10                 82
  PRESENT                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  17Q LOSS MUTATED             0        17     1
  17Q LOSS WILD-TYPE           5        83     1
D72V36, multiclass
             clus
vv            17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 17                 83
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V37, continuous
D72V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  17Q LOSS MUTATED         0        0         0         1        5        10
  17Q LOSS WILD-TYPE       5        1         1         0       29        67
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  17Q LOSS MUTATED           5        1         1          0          0
  17Q LOSS WILD-TYPE        32        3         7          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  17Q LOSS MUTATED           2         0          1          8         1
  17Q LOSS WILD-TYPE        42         1          2         34         6
                    vv
clus                 STAGE IVB
  17Q LOSS MUTATED           1
  17Q LOSS WILD-TYPE        11
D72V39, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 1                  0
  STAGE IB                  5                 29
  STAGE IB1                10                 67
  STAGE IB2                 5                 32
  STAGE II                  1                  3
  STAGE IIA                 1                  7
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 2                 42
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                8                 34
  STAGE IVA                 1                  6
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    40  12
  18P LOSS WILD-TYPE 171  55
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                52                226 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                 55 
$`18P LOSS MUTATED`
TCGA-C5-A1BJ TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML 
      144.16        31.40        35.01        35.61         0.46        20.91 
TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A7CH 
       40.93        73.45        78.35        38.43        33.24       154.32 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DG-A2KM TCGA-DS-A0VN TCGA-EA-A1QS TCGA-EA-A1QT 
       13.61         2.73        63.98        95.67        39.55        40.87 
TCGA-EA-A43B TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK 
       26.01        12.59        26.27         6.64         1.51         0.39 
TCGA-EK-A3GM TCGA-EX-A1H6 TCGA-EX-A69L TCGA-FU-A3EO TCGA-FU-A770 TCGA-HM-A3JJ 
        0.76         7.92        19.79        16.11         1.12        21.67 
TCGA-JW-A5VI TCGA-JW-A69B TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA41 TCGA-Q1-A5R1 
       24.56        28.37        12.49        13.35         8.35        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A73P TCGA-UC-A7PD TCGA-VS-A8EC TCGA-VS-A8EL TCGA-VS-A8Q9 
       16.41        15.88        11.67        46.52        65.49        53.59 
TCGA-VS-A8QH TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A9UI TCGA-VS-A9UQ 
       39.78        33.37        40.14        58.45        45.11        41.52 
TCGA-VS-A9UZ TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-ZJ-AAX4 
       67.20        18.25        17.75         0.69 

$`18P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       68.84        18.74        36.56       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME 
        5.46        19.86        67.46        46.32        30.21        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       53.16        38.99         2.43         3.58        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       83.05       100.14        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      210.67       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC 
       17.19       155.77       131.11        94.95         9.34        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR 
       45.83         8.35       146.86        99.91        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       20.81        20.91        14.73         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        87.75        58.88        36.76        55.63        69.96 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ 
       22.98        16.83        16.18        17.52         8.28        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
       30.90        31.53        31.36        13.05        25.02        36.89 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       26.40        24.56        31.73         0.30        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        25.91        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2H0 TCGA-EK-A2PI TCGA-EK-A2PL 
       24.00        13.48         0.36        60.72        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC 
        0.59         0.36         1.45         0.13        40.96         4.31 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.10         0.43        47.77         0.53         0.10         0.49 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-EX-A8YF 
        0.03        20.35        15.22        14.70         8.32        15.55 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22        23.84        19.04        31.36        36.26        20.98 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
       26.14         1.48        16.14        28.31        14.01        35.44 
TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
       10.55        17.75        25.41        16.57        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        9.44       147.39       137.16        66.81       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ 
       21.44        20.48        15.58         8.28        18.15        21.11 
TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U2 
      209.59        44.61        20.91        11.28         0.89         0.30 
TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA42 
        0.82        22.52        19.56        17.82        19.56         8.52 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
       20.84        17.23         2.96        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       17.56        14.07         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
       14.60        93.99        12.16        69.50        10.03        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC 
       32.42        23.97        19.96        32.15        36.13        11.51 
TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A953 
       59.18        31.27        40.87        16.64         4.73        15.68 
TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 
       56.35        55.50        50.14        51.32        50.47        43.40 
TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH 
       48.39        28.50        29.95        27.12        24.30        46.92 
TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UR 
        1.71        14.53        27.25        47.87        47.47        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 TCGA-VS-A9V1 
       15.85        14.53         3.42        18.25        18.84         5.16 
TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ 
        4.34        16.24        15.42        26.01        29.26        67.59 
TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         1.41         0.16         3.91 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.39               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            154.32             210.67 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             26.14              22.57 
[1] "0.4 - 154.3 (26.1)" "0.0 - 210.7 (22.6)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED    24  10   4   1
  18P LOSS WILD-TYPE 111  60  17   7
D73V3, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               24                111
  T2               10                 60
  T3                4                 17
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V4, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    22   9
  18P LOSS WILD-TYPE 107  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     22    9
  18P LOSS WILD-TYPE  107   47
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               22                107
  1                9                 47
[1] 2 2
[1] FALSE
D73V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   18  1
  18P LOSS WILD-TYPE 90  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     18    1
  18P LOSS WILD-TYPE   90    9
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               18                 90
  1                1                  9
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     9  19
  18P LOSS WILD-TYPE  46 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      9   19
  18P LOSS WILD-TYPE   46  104
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 9                 46
  YES               19                104
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED               0                               38
  18P LOSS WILD-TYPE             6                              204
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18P LOSS MUTATED                                               1
  18P LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18P LOSS MUTATED                                    10
  18P LOSS WILD-TYPE                                  11
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18P LOSS MUTATED                                           0
  18P LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18P LOSS MUTATED                                              6
  18P LOSS WILD-TYPE                                           11
D73V7, multiclass
                                               clus
vv                                              18P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         10
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 6
                                               clus
vv                                              18P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             204
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V8, continuous
D73V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  2     3
  18P LOSS WILD-TYPE                                6    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED                           6
  18P LOSS WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           0    40
  18P LOSS WILD-TYPE                                         2   162
D73V10, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                6                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   40                162
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     4  28
  18P LOSS WILD-TYPE  19 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4   28
  18P LOSS WILD-TYPE   19  134
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 19
  NOT HISPANIC OR LATINO               28                134
[1] 2 2
[1] FALSE
D73V12, continuous
D73V13, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    33  14
  18P LOSS WILD-TYPE 150  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     33   14
  18P LOSS WILD-TYPE  150   60
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  TUMOR FREE               33                150
  WITH TUMOR               14                 60
[1] 2 2
[1] FALSE
                    vv
clus                 G1 G2 G3 G4 GX
  18P LOSS MUTATED    2 30 20  0  2
  18P LOSS WILD-TYPE 16 99 95  1 22
D73V14, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  G1                2                 16
  G2               30                 99
  G3               20                 95
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, continuous
D73V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18P LOSS MUTATED                                             4
  18P LOSS WILD-TYPE                                          34
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  18P LOSS MUTATED                                        0
  18P LOSS WILD-TYPE                                      9
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  18P LOSS MUTATED                                                 0
  18P LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18P LOSS MUTATED               11                  30
  18P LOSS WILD-TYPE             51                 113
D73V17, multiclass
                                                 clus
vv                                                18P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                11
  LIFELONG NON-SMOKER                                           30
                                                 clus
vv                                                18P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     34
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  51
  LIFELONG NON-SMOKER                                            113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V18, continuous
D73V19, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    8  0
  18P LOSS WILD-TYPE 17  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      8    0
  18P LOSS WILD-TYPE   17    3
                         clus
vv                        18P LOSS MUTATED 18P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   8                 17
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D73V20, continuous
D73V21, continuous
D73V22, continuous
D73V23, continuous
D73V24, continuous
D73V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  18P LOSS MUTATED                                     0
  18P LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  18P LOSS MUTATED                                     0
  18P LOSS WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  18P LOSS MUTATED                         7                       0
  18P LOSS WILD-TYPE                      29                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18P LOSS MUTATED                         2
  18P LOSS WILD-TYPE                       6
D73V26, multiclass
                                     clus
vv                                    18P LOSS MUTATED 18P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            7                 29
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  18P LOSS MUTATED                                               0
  18P LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18P LOSS MUTATED                                                6
  18P LOSS WILD-TYPE                                             19
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18P LOSS MUTATED                                                                                  16
  18P LOSS WILD-TYPE                                                                                66
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18P LOSS MUTATED                                                                                             22
  18P LOSS WILD-TYPE                                                                                           99
D73V27, multiclass
                                                                                              clus
vv                                                                                             18P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               22
                                                                                              clus
vv                                                                                             18P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            66
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V28, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   16  8
  18P LOSS WILD-TYPE 55 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     16    8
  18P LOSS WILD-TYPE   55   66
         clus
vv        18P LOSS MUTATED 18P LOSS WILD-TYPE
  ABSENT                16                 55
  PRESENT                8                 66
[1] 2 2
[1] FALSE
D73V29, continuous
D73V30, continuous
D73V31, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     6  17
  18P LOSS WILD-TYPE  43 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6   17
  18P LOSS WILD-TYPE   43  100
                                          clus
vv                                         18P LOSS MUTATED 18P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 43
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               17                100
[1] 2 2
[1] FALSE
D73V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18P LOSS MUTATED              3          19         14
  18P LOSS WILD-TYPE           12          35         71
D73V33, multiclass
              clus
vv             18P LOSS MUTATED 18P LOSS WILD-TYPE
  CURRENT USER                3                 12
  FORMER USER                19                 35
  NEVER USED                 14                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V34, continuous
D73V35, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   17  0
  18P LOSS WILD-TYPE 75 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     17    0
  18P LOSS WILD-TYPE   75   18
         clus
vv        18P LOSS MUTATED 18P LOSS WILD-TYPE
  ABSENT                17                 75
  PRESENT                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  18P LOSS MUTATED             1        15     2
  18P LOSS WILD-TYPE           4        85     0
D73V36, multiclass
             clus
vv            18P LOSS MUTATED 18P LOSS WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 15                 85
  OTHER                      2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V37, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                 15 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MP 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-GH-A9DA         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3Q8         TCGA-MA-AA3W 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MA-AA3Z         TCGA-MA-AA42         TCGA-MU-A51Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-MY-A913         TCGA-ZX-AA5X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D73V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  18P LOSS MUTATED         0        0         0         0        6        22
  18P LOSS WILD-TYPE       5        1         1         1       28        55
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  18P LOSS MUTATED           5        2         1          0          0
  18P LOSS WILD-TYPE        32        2         7          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  18P LOSS MUTATED           9         0          1          5         0
  18P LOSS WILD-TYPE        35         1          2         37         7
                    vv
clus                 STAGE IVB
  18P LOSS MUTATED           2
  18P LOSS WILD-TYPE        10
D73V39, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  6                 28
  STAGE IB1                22                 55
  STAGE IB2                 5                 32
  STAGE II                  2                  2
  STAGE IIA                 1                  7
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 9                 35
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                5                 37
  STAGE IVA                 0                  7
  STAGE IVB                 2                 10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    51  19
  18Q LOSS WILD-TYPE 160  48
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                70                208 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                19                 48 
$`18Q LOSS MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML 
       31.40        35.01        57.73        35.61         0.46        20.91 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A7CH TCGA-C5-A7UC 
       40.93        78.35        38.43        33.24       154.32        17.19 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A8XK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DS-A0VN 
       13.61         2.73        99.91        63.98        87.75        95.67 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A43B TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2H0 
       39.55        40.87        26.01        14.89        12.59        60.72 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PM TCGA-EK-A3GM 
       26.27         6.64         1.51         0.39         0.59         0.76 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A3EO TCGA-FU-A770 TCGA-HM-A3JJ TCGA-IR-A3LA 
        7.92        15.22        16.11         1.12        21.67       137.16 
TCGA-IR-A3LB TCGA-IR-A3LH TCGA-JW-A5VI TCGA-JW-A69B TCGA-JX-A3PZ TCGA-LP-A4AW 
       66.81        78.71        24.56        28.37        21.11         0.89 
TCGA-LP-A4AX TCGA-LP-A7HU TCGA-MA-AA41 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       12.49        13.35         8.35        15.58        16.41         9.04 
TCGA-Q1-A73P TCGA-RA-A741 TCGA-UC-A7PD TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EJ 
       15.88        14.60        11.67        10.03        46.52        19.96 
TCGA-VS-A8EL TCGA-VS-A8Q9 TCGA-VS-A8QH TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A959 
       65.49        53.59        39.78        40.14        58.45        51.32 
TCGA-VS-A9U6 TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UO TCGA-VS-A9UQ TCGA-VS-A9UZ 
       43.40        24.30        45.11        47.87        41.52        67.20 
TCGA-VS-A9V1 TCGA-VS-A9V3 TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 
        5.16        17.75        67.59         0.69 

$`18Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
       82.85         5.46        19.86        67.46        46.32        30.21 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       53.16        38.99         2.43         3.58        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       73.45        83.05       100.14        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       210.67       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7XC 
      147.35       155.77       131.11        94.95         9.34        50.99 
TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
       45.83         8.35       146.86        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL 
       20.91        14.73         1.12        95.11        82.06        44.94 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76        55.63        69.96        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18        17.52         8.28        37.35        30.90        31.53 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
       31.36        13.05        25.02        36.89        26.40        24.56 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       31.73         0.30        24.82         7.46        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       27.29        27.25        27.22        24.00        13.48         0.36 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA 
       19.27         0.43         0.36         1.45         0.13        40.96 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ 
        4.31         0.10         0.43        47.77         0.53         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.49         0.03        20.35        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
       15.55         1.22        23.84        19.04        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       20.98        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK 
       35.44        10.55        17.75        25.41        16.57        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
       14.93         9.44       147.39       129.37        96.95        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VJ TCGA-JW-A5VK 
       29.85        36.36        27.42         3.29        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV 
       15.58         8.28        18.15       209.59        44.61        20.91 
TCGA-LP-A4AU TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
       11.28         0.30         0.82        22.52        19.56        17.82 
TCGA-MA-AA3Z TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
       19.56         8.52        11.38        28.08        34.62        19.96 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R3 
       54.81        35.05        20.84        17.23         2.96        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       16.14        17.56        14.07         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EG TCGA-VS-A8EH 
       19.59        93.99        12.16        69.50        45.57        32.42 
TCGA-VS-A8EI TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       23.97        32.15        36.13        11.51        59.18        31.27 
TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A94Z TCGA-VS-A953 TCGA-VS-A954 
       40.87        16.64         4.73        33.37        15.68        56.35 
TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A9U5 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       55.50        50.14        50.47        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP 
       27.12        46.92         1.71        14.53        27.25        47.47 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9V0 
       26.07        15.85        14.53         3.42        18.25        18.84 
TCGA-VS-A9V2 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       18.25         4.34        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         1.41         0.16         3.91 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.39               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            154.32             210.67 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            25.285             22.570 
[1] "0.4 - 154.3 (25.3)" "0.0 - 210.7 (22.6)"
[1] "hr=" "1.2"
D74V2, continuous
                    vv
clus                  T1  T2  T3  T4
  18Q LOSS MUTATED    30  14   7   2
  18Q LOSS WILD-TYPE 105  56  14   6
D74V3, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               30                105
  T2               14                 56
  T3                7                 14
  T4                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V4, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   32  8
  18Q LOSS WILD-TYPE 97 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     32    8
  18Q LOSS WILD-TYPE   97   48
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               32                 97
  1                8                 48
[1] 2 2
[1] FALSE
D74V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   28  4
  18Q LOSS WILD-TYPE 80  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     28    4
  18Q LOSS WILD-TYPE   80    6
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               28                 80
  1                4                  6
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   12 31
  18Q LOSS WILD-TYPE 43 92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     12   31
  18Q LOSS WILD-TYPE   43   92
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                12                 43
  YES               31                 92
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED               0                               50
  18Q LOSS WILD-TYPE             6                              192
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18Q LOSS MUTATED                                               1
  18Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18Q LOSS MUTATED                                    12
  18Q LOSS WILD-TYPE                                   9
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18Q LOSS MUTATED                                           2
  18Q LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18Q LOSS MUTATED                                              8
  18Q LOSS WILD-TYPE                                            9
D74V7, multiclass
                                               clus
vv                                              18Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 8
                                               clus
vv                                              18Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             192
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                            9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V8, continuous
D74V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  2     4
  18Q LOSS WILD-TYPE                                6    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED                           7
  18Q LOSS WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           0    55
  18Q LOSS WILD-TYPE                                         2   147
D74V10, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                                7                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   55                147
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4  35
  18Q LOSS WILD-TYPE  19 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4   35
  18Q LOSS WILD-TYPE   19  127
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 19
  NOT HISPANIC OR LATINO               35                127
[1] 2 2
[1] FALSE
D74V12, continuous
D74V13, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    43  22
  18Q LOSS WILD-TYPE 140  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     43   22
  18Q LOSS WILD-TYPE  140   52
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  TUMOR FREE               43                140
  WITH TUMOR               22                 52
[1] 2 2
[1] FALSE
                    vv
clus                 G1 G2 G3 G4 GX
  18Q LOSS MUTATED    4 31 29  1  7
  18Q LOSS WILD-TYPE 14 98 86  0 17
D74V14, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  G1                4                 14
  G2               31                 98
  G3               29                 86
  G4                1                  0
  GX                7                 17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, continuous
D74V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18Q LOSS MUTATED                                             5
  18Q LOSS WILD-TYPE                                          33
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  18Q LOSS MUTATED                                        1
  18Q LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  18Q LOSS MUTATED                                                 0
  18Q LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18Q LOSS MUTATED               14                  39
  18Q LOSS WILD-TYPE             48                 104
D74V17, multiclass
                                                 clus
vv                                                18Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                14
  LIFELONG NON-SMOKER                                           39
                                                 clus
vv                                                18Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     33
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  48
  LIFELONG NON-SMOKER                                            104
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V18, continuous
D74V19, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    7  1
  18Q LOSS WILD-TYPE 18  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7    1
  18Q LOSS WILD-TYPE   18    2
                         clus
vv                        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   7                 18
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D74V20, continuous
D74V21, continuous
D74V22, continuous
D74V23, continuous
D74V24, continuous
D74V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  18Q LOSS MUTATED                                     0
  18Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  18Q LOSS MUTATED                                     0
  18Q LOSS WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  18Q LOSS MUTATED                         8                       0
  18Q LOSS WILD-TYPE                      28                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18Q LOSS MUTATED                         3
  18Q LOSS WILD-TYPE                       5
D74V26, multiclass
                                     clus
vv                                    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            8                 28
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  18Q LOSS MUTATED                                               0
  18Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18Q LOSS MUTATED                                                7
  18Q LOSS WILD-TYPE                                             18
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18Q LOSS MUTATED                                                                                  25
  18Q LOSS WILD-TYPE                                                                                57
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18Q LOSS MUTATED                                                                                             28
  18Q LOSS WILD-TYPE                                                                                           93
D74V27, multiclass
                                                                                              clus
vv                                                                                             18Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               28
                                                                                              clus
vv                                                                                             18Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            57
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V28, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   19 11
  18Q LOSS WILD-TYPE 52 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     19   11
  18Q LOSS WILD-TYPE   52   63
         clus
vv        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ABSENT                19                 52
  PRESENT               11                 63
[1] 2 2
[1] FALSE
D74V29, continuous
D74V30, continuous
D74V31, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   10 23
  18Q LOSS WILD-TYPE 39 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     10   23
  18Q LOSS WILD-TYPE   39   94
                                          clus
vv                                         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   10                 39
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               23                 94
[1] 2 2
[1] FALSE
D74V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18Q LOSS MUTATED              4          21         22
  18Q LOSS WILD-TYPE           11          33         63
D74V33, multiclass
              clus
vv             18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CURRENT USER                4                 11
  FORMER USER                21                 33
  NEVER USED                 22                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V34, continuous
D74V35, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   24  0
  18Q LOSS WILD-TYPE 68 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     24    0
  18Q LOSS WILD-TYPE   68   18
         clus
vv        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ABSENT                24                 68
  PRESENT                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  18Q LOSS MUTATED             1        25     2
  18Q LOSS WILD-TYPE           4        75     0
D74V36, multiclass
             clus
vv            18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CARBOPLATIN                1                  4
  CISPLATIN                 25                 75
  OTHER                      2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V37, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 15 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MP 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-GH-A9DA         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-JW-A852         TCGA-JX-A3Q8         TCGA-MA-AA3W 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-MA-AA3Z         TCGA-MA-AA42         TCGA-MU-A51Y 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-MY-A913         TCGA-ZX-AA5X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D74V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  18Q LOSS MUTATED         1        1         0         0        8        24
  18Q LOSS WILD-TYPE       4        0         1         1       26        53
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  18Q LOSS MUTATED           5        2         1          2          0
  18Q LOSS WILD-TYPE        32        2         7          3          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  18Q LOSS MUTATED          14         0          2          6         0
  18Q LOSS WILD-TYPE        30         1          1         36         7
                    vv
clus                 STAGE IVB
  18Q LOSS MUTATED           4
  18Q LOSS WILD-TYPE         8
D74V39, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  1                  0
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  8                 26
  STAGE IB1                24                 53
  STAGE IB2                 5                 32
  STAGE II                  2                  2
  STAGE IIA                 1                  7
  STAGE IIA1                2                  3
  STAGE IIA2                0                  7
  STAGE IIB                14                 30
  STAGE III                 0                  1
  STAGE IIIA                2                  1
  STAGE IIIB                6                 36
  STAGE IVA                 0                  7
  STAGE IVB                 4                  8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    34  23
  19P LOSS WILD-TYPE 177  44
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                57                221 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                23                 44 
$`19P LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       23.67         5.46        31.40        30.21        35.01        57.73 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A7CO TCGA-C5-A7X3 
       35.61         0.46        20.91        40.93       147.35         9.34 
TCGA-C5-A7X8 TCGA-C5-A8XH TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DS-A0VN 
        2.73        45.83        99.91        23.51        27.52        95.67 
TCGA-EA-A1QT TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EK-A2IP 
       40.87        36.89        24.56        31.73        26.01         6.64 
TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2R8 TCGA-EK-A2RA TCGA-EK-A3GJ 
       19.27         0.39         0.43         1.45        40.96         0.10 
TCGA-EK-A3GM TCGA-EX-A69L TCGA-FU-A23L TCGA-GH-A9DA TCGA-IR-A3LC TCGA-JW-A5VK 
        0.76        19.79        23.84        17.75       129.37        20.48 
TCGA-JX-A3PZ TCGA-JX-A5QV TCGA-PN-A8MA TCGA-Q1-A6DT TCGA-Q1-A73S TCGA-RA-A741 
       21.11        20.91         2.96         9.04        22.62        14.60 
TCGA-VS-A8EB TCGA-VS-A8EJ TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A957 
       10.03        19.96        39.78        16.64         4.73        55.50 
TCGA-VS-A9UD TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UP TCGA-VS-A9V0 
       24.30        45.11        14.53        27.25        47.47        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V4 TCGA-ZJ-AAX4 
        5.16         4.34         0.69 

$`19P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        49.48        57.04        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK 
       19.86        67.46        46.32        53.16        38.99         2.43 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
        3.58        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43        33.24        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       20.42       210.67       154.32       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 
       20.35        17.19       155.77       131.11        94.95        13.61 
TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
       50.99         8.35       146.86        20.81        20.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL 
        1.12        95.11        82.06        44.94        63.98        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76        55.63        69.96        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18        17.52         8.28        39.55        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A44S 
       31.53        31.36        13.05        25.02        26.40         0.30 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       27.25        27.22        24.00        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 
       60.72        26.27         1.51         0.59         0.36         0.13 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK 
        4.31         0.10         0.43        47.77         0.53         0.49 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M 
        0.03        20.35         7.92        15.22        14.70         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       15.55         1.22        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       20.98        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44        10.55         1.12        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        21.44        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       18.15       209.59        44.61        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        19.56        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         8.35         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-Q1-A5R1 
       19.96        54.81        35.05        20.84        17.23        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       16.41        15.95        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
        9.34        18.64        19.59        11.67        93.99        12.16 
TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EL 
       69.50        46.52        45.57        32.42        23.97        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM 
       32.15        53.59        36.13        11.51        59.18        31.27 
TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 
       40.87        33.37        40.14        58.45        15.68        56.35 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UQ 
       29.95        27.12        46.92         1.71        47.87        41.52 
TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       26.07        15.85        14.53         3.42        18.25        67.20 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ 
       18.25        17.75        16.24        15.42        26.01        29.26 
TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       67.59        19.13         1.41         0.16         3.91 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.10               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            147.35             210.67 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             21.11              24.00 
[1] "0.1 - 147.3 (21.1)" "0.0 - 210.7 (24.0)"
[1] "hr=" "2.4"
D75V2, continuous
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED    26  11   7   1
  19P LOSS WILD-TYPE 109  59  14   7
D75V3, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               26                109
  T2               11                 59
  T3                7                 14
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V4, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    25   6
  19P LOSS WILD-TYPE 104  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     25    6
  19P LOSS WILD-TYPE  104   50
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               25                104
  1                6                 50
[1] 2 2
[1] FALSE
D75V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   20  2
  19P LOSS WILD-TYPE 88  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     20    2
  19P LOSS WILD-TYPE   88    8
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               20                 88
  1                2                  8
[1] 2 2
[1] FALSE
D75V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   12 26
  19P LOSS WILD-TYPE 43 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     12   26
  19P LOSS WILD-TYPE   43   97
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                12                 43
  YES               26                 97
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED               1                               48
  19P LOSS WILD-TYPE             5                              194
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19P LOSS MUTATED                                               1
  19P LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19P LOSS MUTATED                                     4
  19P LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19P LOSS MUTATED                                           0
  19P LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19P LOSS MUTATED                                              6
  19P LOSS WILD-TYPE                                           11
D75V7, multiclass
                                               clus
vv                                              19P LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            48
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 6
                                               clus
vv                                              19P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             194
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V8, continuous
D75V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     2
  19P LOSS WILD-TYPE                                8    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED                           5
  19P LOSS WILD-TYPE                        23
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           1    49
  19P LOSS WILD-TYPE                                         1   153
D75V10, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                5                 23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  1
  WHITE                                                   49                153
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2  33
  19P LOSS WILD-TYPE  21 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   33
  19P LOSS WILD-TYPE   21  129
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 21
  NOT HISPANIC OR LATINO               33                129
[1] 2 2
[1] FALSE
D75V12, continuous
D75V13, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    28  23
  19P LOSS WILD-TYPE 155  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     28   23
  19P LOSS WILD-TYPE  155   51
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  TUMOR FREE               28                155
  WITH TUMOR               23                 51
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  19P LOSS MUTATED     1  23  29   0   5
  19P LOSS WILD-TYPE  17 106  86   1  19
D75V14, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  G1                1                 17
  G2               23                106
  G3               29                 86
  G4                0                  1
  GX                5                 19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V15, continuous
D75V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19P LOSS MUTATED                                             9
  19P LOSS WILD-TYPE                                          29
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  19P LOSS MUTATED                                        2
  19P LOSS WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  19P LOSS MUTATED                                                 0
  19P LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19P LOSS MUTATED               11                  28
  19P LOSS WILD-TYPE             51                 115
D75V17, multiclass
                                                 clus
vv                                                19P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                11
  LIFELONG NON-SMOKER                                           28
                                                 clus
vv                                                19P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     29
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  51
  LIFELONG NON-SMOKER                                            115
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V18, continuous
D75V19, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    7  0
  19P LOSS WILD-TYPE 18  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7    0
  19P LOSS WILD-TYPE   18    3
                         clus
vv                        19P LOSS MUTATED 19P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   7                 18
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D75V20, continuous
D75V21, continuous
D75V22, continuous
D75V23, continuous
D75V24, continuous
D75V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  19P LOSS MUTATED                                     0
  19P LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  19P LOSS MUTATED                                     1
  19P LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  19P LOSS MUTATED                         7                       0
  19P LOSS WILD-TYPE                      29                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19P LOSS MUTATED                         1
  19P LOSS WILD-TYPE                       7
D75V26, multiclass
                                     clus
vv                                    19P LOSS MUTATED 19P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                            7                 29
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  19P LOSS MUTATED                                               1
  19P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  19P LOSS MUTATED                                                3
  19P LOSS WILD-TYPE                                             22
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19P LOSS MUTATED                                                                                  17
  19P LOSS WILD-TYPE                                                                                65
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19P LOSS MUTATED                                                                                             21
  19P LOSS WILD-TYPE                                                                                          100
D75V27, multiclass
                                                                                              clus
vv                                                                                             19P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          17
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               21
                                                                                              clus
vv                                                                                             19P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            65
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V28, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   13 12
  19P LOSS WILD-TYPE 58 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     13   12
  19P LOSS WILD-TYPE   58   62
         clus
vv        19P LOSS MUTATED 19P LOSS WILD-TYPE
  ABSENT                13                 58
  PRESENT               12                 62
[1] 2 2
[1] FALSE
D75V29, continuous
D75V30, continuous
D75V31, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    9 21
  19P LOSS WILD-TYPE 40 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9   21
  19P LOSS WILD-TYPE   40   96
                                          clus
vv                                         19P LOSS MUTATED 19P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               21                 96
[1] 2 2
[1] FALSE
D75V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19P LOSS MUTATED              2           8         19
  19P LOSS WILD-TYPE           13          46         66
D75V33, multiclass
              clus
vv             19P LOSS MUTATED 19P LOSS WILD-TYPE
  CURRENT USER                2                 13
  FORMER USER                 8                 46
  NEVER USED                 19                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V34, continuous
D75V35, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   16  5
  19P LOSS WILD-TYPE 76 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     16    5
  19P LOSS WILD-TYPE   76   13
         clus
vv        19P LOSS MUTATED 19P LOSS WILD-TYPE
  ABSENT                16                 76
  PRESENT                5                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  19P LOSS MUTATED             0        22     1
  19P LOSS WILD-TYPE           5        78     1
D75V36, multiclass
             clus
vv            19P LOSS MUTATED 19P LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 22                 78
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V37, continuous
D75V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  19P LOSS MUTATED         1        0         0         0        6        21
  19P LOSS WILD-TYPE       4        1         1         1       28        56
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  19P LOSS MUTATED           7        1         2          2          1
  19P LOSS WILD-TYPE        30        3         6          3          6
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  19P LOSS MUTATED           7         0          1          7         1
  19P LOSS WILD-TYPE        37         1          2         35         6
                    vv
clus                 STAGE IVB
  19P LOSS MUTATED           2
  19P LOSS WILD-TYPE        10
D75V39, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  6                 28
  STAGE IB1                21                 56
  STAGE IB2                 7                 30
  STAGE II                  1                  3
  STAGE IIA                 2                  6
  STAGE IIA1                2                  3
  STAGE IIA2                1                  6
  STAGE IIB                 7                 37
  STAGE III                 0                  1
  STAGE IIIA                1                  2
  STAGE IIIB                7                 35
  STAGE IVA                 1                  6
  STAGE IVB                 2                 10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    19  10
  19Q LOSS WILD-TYPE 192  57
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                29                249 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                10                 57 
$`19Q LOSS MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1ML TCGA-C5-A7X8 
       31.40        30.21        35.01         0.46        20.91         2.73 
TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EK-A2IP TCGA-EK-A2PI 
       99.91        23.51        95.67        40.87         6.64        19.27 
TCGA-EK-A3GJ TCGA-EK-A3GM TCGA-FU-A23L TCGA-GH-A9DA TCGA-IR-A3LC TCGA-JW-A5VK 
        0.10         0.76        23.84        17.75       129.37        20.48 
TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-Q1-A6DT TCGA-VS-A8EH TCGA-VS-A8EJ TCGA-VS-A8QH 
       44.61        20.91         9.04        32.42        19.96        39.78 
TCGA-VS-A957 TCGA-VS-A9UM TCGA-VS-A9V0 TCGA-VS-A9V4 TCGA-ZJ-AAX4 
       55.50        27.25        18.84         4.34         0.69 

$`19Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1ME 
       82.85         5.46        19.86        67.46        46.32        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16        38.99        35.61         2.43        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       44.22        73.18        73.45        83.05        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43        33.24        52.01        18.02        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      210.67       154.32       101.82       134.33        15.48        20.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      147.35        17.19       155.77       131.11        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YR 
       13.61        50.99        45.83         8.35       146.86        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       20.81        20.91        14.73         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       44.94        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       69.96        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       25.02        36.89        26.40        24.56        31.73        26.01 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        0.30        24.82         7.46        14.89        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N 
       27.29        27.25        27.22        24.00        13.48         0.36 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL 
       12.59        60.72        26.27         1.51         0.39         0.43 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC 
        0.59         0.36         1.45         0.13        40.96         4.31 
TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN 
        0.10         0.43        47.77         0.53         0.49         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92        15.22        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
       15.55         1.22        19.04        16.11        31.36        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       20.98        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44        10.55         1.12        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        29.85        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
        3.29        24.56        21.44        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       18.15        21.11       209.59        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        19.56        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         8.35         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA 
       19.96        54.81        35.05        20.84        17.23         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       15.58        16.41        15.95        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC 
       11.67        93.99        12.16        69.50        10.03        46.52 
TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA 
       45.57        23.97        65.49        32.15        53.59        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Y 
       11.51        59.18        31.27        40.87        16.64         4.73 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 
       33.37        40.14        58.45        15.68        56.35        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       51.32        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL 
       27.12        24.30        46.92        45.11         1.71        14.53 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       47.87        47.47        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 
        3.42        18.25        67.20         5.16        18.25        17.75 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.10               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            129.37             210.67 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             20.91              23.67 
[1] "0.1 - 129.4 (20.9)" "0.0 - 210.7 (23.7)"
[1] "hr=" "1.7"
D76V2, continuous
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED    13   4   3   1
  19Q LOSS WILD-TYPE 122  66  18   7
D76V3, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               13                122
  T2                4                 66
  T3                3                 18
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    12   2
  19Q LOSS WILD-TYPE 117  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     12    2
  19Q LOSS WILD-TYPE  117   54
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               12                117
  1                2                 54
[1] 2 2
[1] FALSE
D76V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     8   1
  19Q LOSS WILD-TYPE 100   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8    1
  19Q LOSS WILD-TYPE  100    9
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                8                100
  1                1                  9
[1] 2 2
[1] FALSE
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     7  12
  19Q LOSS WILD-TYPE  48 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      7   12
  19Q LOSS WILD-TYPE   48  111
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 7                 48
  YES               12                111
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED               0                               21
  19Q LOSS WILD-TYPE             6                              221
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19Q LOSS MUTATED                                               0
  19Q LOSS WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19Q LOSS MUTATED                                     4
  19Q LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19Q LOSS MUTATED                                           0
  19Q LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19Q LOSS MUTATED                                              4
  19Q LOSS WILD-TYPE                                           13
D76V7, multiclass
                                               clus
vv                                              19Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            21
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 4
                                               clus
vv                                              19Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             221
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V8, continuous
D76V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     1
  19Q LOSS WILD-TYPE                                8    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED                           3
  19Q LOSS WILD-TYPE                        25
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           1    22
  19Q LOSS WILD-TYPE                                         1   180
D76V10, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  8
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                3                 25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  1
  WHITE                                                   22                180
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  12
  19Q LOSS WILD-TYPE  22 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   12
  19Q LOSS WILD-TYPE   22  150
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 22
  NOT HISPANIC OR LATINO               12                150
[1] 2 2
[1] FALSE
D76V12, continuous
D76V13, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    15  10
  19Q LOSS WILD-TYPE 168  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     15   10
  19Q LOSS WILD-TYPE  168   64
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  TUMOR FREE               15                168
  WITH TUMOR               10                 64
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  19Q LOSS MUTATED     0  12  16   0   1
  19Q LOSS WILD-TYPE  18 117  99   1  23
D76V14, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  G1                0                 18
  G2               12                117
  G3               16                 99
  G4                0                  1
  GX                1                 23
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V15, continuous
D76V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19Q LOSS MUTATED                                             3
  19Q LOSS WILD-TYPE                                          35
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  19Q LOSS MUTATED                                        1
  19Q LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  19Q LOSS MUTATED                                                 0
  19Q LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19Q LOSS MUTATED                5                  16
  19Q LOSS WILD-TYPE             57                 127
D76V17, multiclass
                                                 clus
vv                                                19Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 5
  LIFELONG NON-SMOKER                                           16
                                                 clus
vv                                                19Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     35
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  57
  LIFELONG NON-SMOKER                                            127
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V18, continuous
D76V19, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    4  0
  19Q LOSS WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4    0
  19Q LOSS WILD-TYPE   21    3
                         clus
vv                        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   4                 21
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D76V20, continuous
D76V21, continuous
D76V22, continuous
D76V23, continuous
D76V24, continuous
D76V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  19Q LOSS MUTATED                                     0
  19Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  19Q LOSS MUTATED                                     0
  19Q LOSS WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  19Q LOSS MUTATED                         5                       0
  19Q LOSS WILD-TYPE                      31                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19Q LOSS MUTATED                         1
  19Q LOSS WILD-TYPE                       7
D76V26, multiclass
                                     clus
vv                                    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            5                 31
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  19Q LOSS MUTATED                                               1
  19Q LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  19Q LOSS MUTATED                                                2
  19Q LOSS WILD-TYPE                                             23
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19Q LOSS MUTATED                                                                                  12
  19Q LOSS WILD-TYPE                                                                                70
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19Q LOSS MUTATED                                                                                              7
  19Q LOSS WILD-TYPE                                                                                          114
D76V27, multiclass
                                                                                              clus
vv                                                                                             19Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                7
                                                                                              clus
vv                                                                                             19Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            70
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V28, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    9  5
  19Q LOSS WILD-TYPE 62 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      9    5
  19Q LOSS WILD-TYPE   62   69
         clus
vv        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ABSENT                 9                 62
  PRESENT                5                 69
[1] 2 2
[1] FALSE
D76V29, continuous
D76V30, continuous
D76V31, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     3   6
  19Q LOSS WILD-TYPE  46 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    6
  19Q LOSS WILD-TYPE   46  111
                                          clus
vv                                         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 46
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                6                111
[1] 2 2
[1] FALSE
D76V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19Q LOSS MUTATED              1           4          9
  19Q LOSS WILD-TYPE           14          50         76
D76V33, multiclass
              clus
vv             19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 4                 50
  NEVER USED                  9                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V34, continuous
D76V35, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   11  1
  19Q LOSS WILD-TYPE 81 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     11    1
  19Q LOSS WILD-TYPE   81   17
         clus
vv        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ABSENT                11                 81
  PRESENT                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  19Q LOSS MUTATED             0        10     1
  19Q LOSS WILD-TYPE           5        90     1
D76V36, multiclass
             clus
vv            19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 10                 90
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V37, continuous
D76V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  19Q LOSS MUTATED         1        0         0         0        3        13
  19Q LOSS WILD-TYPE       4        1         1         1       31        64
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  19Q LOSS MUTATED           2        1         1          1          0
  19Q LOSS WILD-TYPE        35        3         7          4          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  19Q LOSS MUTATED           2         0          0          2         1
  19Q LOSS WILD-TYPE        42         1          3         40         6
                    vv
clus                 STAGE IVB
  19Q LOSS MUTATED           1
  19Q LOSS WILD-TYPE        11
D76V39, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  3                 31
  STAGE IB1                13                 64
  STAGE IB2                 2                 35
  STAGE II                  1                  3
  STAGE IIA                 1                  7
  STAGE IIA1                1                  4
  STAGE IIA2                0                  7
  STAGE IIB                 2                 42
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB                2                 40
  STAGE IVA                 1                  6
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    15   6
  20P LOSS WILD-TYPE 196  61
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                21                257 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                 61 
$`20P LOSS MUTATED`
TCGA-BI-A0VR TCGA-C5-A1ME TCGA-C5-A8XH TCGA-DG-A2KK TCGA-EA-A1QT TCGA-EK-A2H0 
       49.48        57.73        45.83        82.06        40.87        60.72 
TCGA-EK-A2PI TCGA-EX-A1H6 TCGA-FU-A3HY TCGA-FU-A770 TCGA-GH-A9DA TCGA-IR-A3LB 
       19.27         7.92        31.36         1.12        17.75        66.81 
TCGA-JW-A5VI TCGA-JX-A5QV TCGA-MY-A913 TCGA-UC-A7PD TCGA-VS-A8Q9 TCGA-VS-A94Y 
       24.56        20.91        17.23        11.67        53.59         4.73 
TCGA-VS-A9V1 TCGA-VS-AA62 TCGA-ZJ-A8QQ 
        5.16        15.42        67.59 

$`20P LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE 
       17.52        17.82        57.04        23.67        11.44        68.84 
TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM 
       18.74        36.56       144.16       177.04       173.29        82.85 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
        5.46        19.86        67.46        31.40        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
       35.01        53.16        38.99        35.61         0.46         2.43 
TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
       20.91        40.93         3.58        44.22        73.18        73.45 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43        33.24        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       18.02        17.85        20.42       210.67       154.32       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48        20.35       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      131.11        94.95         9.34        13.61         2.73        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-C5-A8YT 
        8.35       146.86        99.91        23.51        27.52        20.81 
TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DG-A2KM 
       20.91        14.73         1.12        95.11        44.94        63.98 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76        55.63        69.96        95.67 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18        17.52         8.28        39.55 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       37.35        30.90        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       36.89        26.40        24.56        31.73        26.01         0.30 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       24.82         7.46        14.89        26.79        25.91        27.29 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       27.25        27.22        24.00        13.48         0.36        12.59 
TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM 
       26.27         6.64         1.51         0.39         0.43         0.59 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD 
        0.36         1.45         0.13        40.96         4.31         0.10 
TCGA-EK-A2RK TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM 
        0.43        47.77         0.53         0.10         0.49         0.76 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03        20.35        15.22        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
       15.55         1.22        23.84        19.04        16.11        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       20.98        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ TCGA-HM-A3JK 
       35.44        10.55        25.41        16.57        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         9.44       147.39       137.16       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH 
       78.71        81.96        29.85        36.36        27.42         3.29 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       21.11       209.59        44.61        11.28         0.89        12.49 
TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y 
        0.30         0.82        13.35        22.52        19.56        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         8.35         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
       19.96        54.81        35.05        20.84         2.96        15.58 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O 
       16.41        15.95         9.04        16.14        17.56        14.07 
TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 
       15.88         9.34        18.64        22.62        19.59        14.60 
TCGA-UC-A7PF TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG 
       93.99        12.16        69.50        10.03        46.52        45.57 
TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA 
       32.42        23.97        19.96        65.49        32.15        36.13 
TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X 
       11.51        59.18        39.78        31.27        40.87        16.64 
TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       33.37        40.14        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       50.14        51.32        50.47        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       29.95        27.12        24.30        46.92        45.11         1.71 
TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR 
       14.53        27.25        47.87        47.47        41.52        26.07 
TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       15.85        14.53         3.42        18.25        67.20        18.84 
TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 TCGA-WL-A834 TCGA-XS-A8TJ 
       18.25        17.75         4.34        16.24        26.01        29.26 
TCGA-ZJ-A8QR TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       19.13         0.69         1.41         0.16         3.91 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1.12               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             82.06             210.67 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             24.56              22.98 
[1] "1.1 - 82.1 (24.6)"  "0.0 - 210.7 (23.0)"
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED    12   6   1   0
  20P LOSS WILD-TYPE 123  64  20   8
D77V3, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               12                123
  T2                6                 64
  T3                1                 20
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V4, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    12   4
  20P LOSS WILD-TYPE 117  52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12    4
  20P LOSS WILD-TYPE  117   52
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               12                117
  1                4                 52
[1] 2 2
[1] FALSE
D77V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    9  1
  20P LOSS WILD-TYPE 99  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9    1
  20P LOSS WILD-TYPE   99    9
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                9                 99
  1                1                  9
[1] 2 2
[1] FALSE
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8  10
  20P LOSS WILD-TYPE  47 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8   10
  20P LOSS WILD-TYPE   47  113
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 8                 47
  YES               10                113
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED               0                               18
  20P LOSS WILD-TYPE             6                              224
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20P LOSS MUTATED                                               1
  20P LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20P LOSS MUTATED                                     3
  20P LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20P LOSS MUTATED                                           0
  20P LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20P LOSS MUTATED                                              1
  20P LOSS WILD-TYPE                                           16
D77V7, multiclass
                                               clus
vv                                              20P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            18
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              20P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             224
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V8, continuous
D77V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  2     1
  20P LOSS WILD-TYPE                                6    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED                           1
  20P LOSS WILD-TYPE                        27
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           0    17
  20P LOSS WILD-TYPE                                         2   185
D77V10, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                1                 27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   17                185
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  11
  20P LOSS WILD-TYPE  21 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   11
  20P LOSS WILD-TYPE   21  151
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 21
  NOT HISPANIC OR LATINO               11                151
[1] 2 2
[1] FALSE
D77V12, continuous
D77V13, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    15   7
  20P LOSS WILD-TYPE 168  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     15    7
  20P LOSS WILD-TYPE  168   67
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  TUMOR FREE               15                168
  WITH TUMOR                7                 67
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  20P LOSS MUTATED     2   9   8   0   2
  20P LOSS WILD-TYPE  16 120 107   1  22
D77V14, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  G1                2                 16
  G2                9                120
  G3                8                107
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V15, continuous
D77V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20P LOSS MUTATED                                             4
  20P LOSS WILD-TYPE                                          34
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  20P LOSS MUTATED                                        1
  20P LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  20P LOSS MUTATED                                                 1
  20P LOSS WILD-TYPE                                               2
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20P LOSS MUTATED                8                   6
  20P LOSS WILD-TYPE             54                 137
D77V17, multiclass
                                                 clus
vv                                                20P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 8
  LIFELONG NON-SMOKER                                            6
                                                 clus
vv                                                20P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     34
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  2
  CURRENT SMOKER                                                  54
  LIFELONG NON-SMOKER                                            137
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V18, continuous
D77V19, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    0  1
  20P LOSS WILD-TYPE 25  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    1
  20P LOSS WILD-TYPE   25    2
                         clus
vv                        20P LOSS MUTATED 20P LOSS WILD-TYPE
  COMPLETED AS PLANNED                   0                 25
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D77V20, continuous
D77V21, continuous
D77V22, continuous
D77V23, continuous
D77V24, continuous
D77V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  20P LOSS MUTATED                                     0
  20P LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  20P LOSS MUTATED                                     0
  20P LOSS WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  20P LOSS MUTATED                         4                       0
  20P LOSS WILD-TYPE                      32                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20P LOSS MUTATED                         0
  20P LOSS WILD-TYPE                       8
D77V26, multiclass
                                     clus
vv                                    20P LOSS MUTATED 20P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  7
  OTHER LOCATION, SPECIFY                            4                 32
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  20P LOSS MUTATED                                               0
  20P LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  20P LOSS MUTATED                                                1
  20P LOSS WILD-TYPE                                             24
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20P LOSS MUTATED                                                                                   6
  20P LOSS WILD-TYPE                                                                                76
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20P LOSS MUTATED                                                                                             11
  20P LOSS WILD-TYPE                                                                                          110
D77V27, multiclass
                                                                                              clus
vv                                                                                             20P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              1
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               11
                                                                                              clus
vv                                                                                             20P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               24
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            76
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V28, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    6  5
  20P LOSS WILD-TYPE 65 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6    5
  20P LOSS WILD-TYPE   65   69
         clus
vv        20P LOSS MUTATED 20P LOSS WILD-TYPE
  ABSENT                 6                 65
  PRESENT                5                 69
[1] 2 2
[1] FALSE
D77V29, continuous
D77V30, continuous
D77V31, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     4   7
  20P LOSS WILD-TYPE  45 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4    7
  20P LOSS WILD-TYPE   45  110
                                          clus
vv                                         20P LOSS MUTATED 20P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 45
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                7                110
[1] 2 2
[1] FALSE
D77V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20P LOSS MUTATED              3           5          5
  20P LOSS WILD-TYPE           12          49         80
D77V33, multiclass
              clus
vv             20P LOSS MUTATED 20P LOSS WILD-TYPE
  CURRENT USER                3                 12
  FORMER USER                 5                 49
  NEVER USED                  5                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V34, continuous
D77V35, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    8  1
  20P LOSS WILD-TYPE 84 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8    1
  20P LOSS WILD-TYPE   84   17
         clus
vv        20P LOSS MUTATED 20P LOSS WILD-TYPE
  ABSENT                 8                 84
  PRESENT                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  20P LOSS MUTATED             0         8     0
  20P LOSS WILD-TYPE           5        92     2
D77V36, multiclass
             clus
vv            20P LOSS MUTATED 20P LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                  8                 92
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V37, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 15 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1ML 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-JX-A3Q8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MA-AA3W         TCGA-MA-AA3Z         TCGA-MA-AA42 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM         TCGA-ZX-AA5X 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D77V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  20P LOSS MUTATED         0        0         0         0        3         7
  20P LOSS WILD-TYPE       5        1         1         1       31        70
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  20P LOSS MUTATED           1        0         1          0          0
  20P LOSS WILD-TYPE        36        4         7          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  20P LOSS MUTATED           6         0          0          4         0
  20P LOSS WILD-TYPE        38         1          3         38         7
                    vv
clus                 STAGE IVB
  20P LOSS MUTATED           1
  20P LOSS WILD-TYPE        11
D77V39, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  3                 31
  STAGE IB1                 7                 70
  STAGE IB2                 1                 36
  STAGE II                  0                  4
  STAGE IIA                 1                  7
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 6                 38
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB                4                 38
  STAGE IVA                 0                  7
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     4   6
  20Q LOSS WILD-TYPE 207  61
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                268 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                 61 
$`20Q LOSS MUTATED`
TCGA-C5-A8XH TCGA-EK-A2PI TCGA-HG-A2PA TCGA-JX-A5QV TCGA-UC-A7PD TCGA-VS-A8EB 
       45.83        19.27        25.41        20.91        11.67        10.03 
TCGA-VS-A94Y TCGA-VS-A9U5 TCGA-VS-A9V1 TCGA-VS-A9V2 
        4.73        50.47         5.16        18.25 

$`20Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN 
       17.52        17.82        49.48        57.04        23.67        11.44 
TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL 
       68.84        18.74        36.56       144.16       177.04       173.29 
TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
       82.85         5.46        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       30.21        35.01        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
        0.46         2.43        20.91        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       73.18        73.45        83.05        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
       33.24        52.01        18.02        17.85        20.42       210.67 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      154.32       101.82       134.33        15.48        20.35       147.35 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19       155.77       131.11        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ 
        2.73        50.99         8.35       146.86        99.91        23.51 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52        20.81        20.91        14.73         1.12        95.11 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       55.63        69.96        95.67        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       17.52         8.28        39.55        40.87        37.35        30.90 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
       31.53        31.36        13.05        25.02        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       24.56        31.73        26.01         0.30        24.82         7.46 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89        26.79        25.91        27.29        27.25        27.22 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2H1 
       24.00        13.48         0.36        12.59        60.72        26.27 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
        6.64         1.51         0.39         0.43         0.59         0.36 
TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK 
        1.45         0.13        40.96         4.31         0.10         0.43 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GM TCGA-EK-A3GN 
       47.77         0.53         0.10         0.49         0.76         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92        15.22        14.70        19.79         8.32 
TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       15.55         1.22        23.84        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
       36.26        20.98        26.14         1.48        16.14        28.31 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A9SC 
       14.01        35.44        10.55         1.12        17.75        16.57 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         9.44       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       129.37        96.95        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       36.36        27.42         3.29        24.56        21.44        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 
       15.58        28.37         8.28        18.15        21.11       209.59 
TCGA-JX-A3Q8 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
       44.61        11.28         0.89        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
       13.35        22.52        19.56        17.82        19.56         8.35 
TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        8.52        11.38        28.08        34.62        19.96        54.81 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       35.05        20.84        17.23         2.96        15.58        16.41 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P 
       15.95         9.04        16.14        17.56        14.07        15.88 
TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        9.34        18.64        22.62        19.59        14.60        93.99 
TCGA-UC-A7PG TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI 
       12.16        69.50        46.52        45.57        32.42        23.97 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC 
       19.96        65.49        32.15        53.59        36.13        11.51 
TCGA-VS-A8QF TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z 
       59.18        39.78        31.27        40.87        16.64        33.37 
TCGA-VS-A950 TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 
       40.14        58.45        15.68        56.35        55.50        50.14 
TCGA-VS-A959 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UC 
       51.32        43.40        48.39        28.50        29.95        27.12 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UM 
       24.30        46.92        45.11         1.71        14.53        27.25 
TCGA-VS-A9UO TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU 
       47.87        47.47        41.52        26.07        15.85        14.53 
TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V3 TCGA-VS-A9V4 
        3.42        18.25        67.20        18.84        17.75         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-A8QR 
       16.24        15.42        26.01        29.26        67.59        19.13 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        0.69         1.41         0.16         3.91 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              4.73               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             50.47             210.67 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            18.760             23.755 
[1] "4.7 - 50.5 (18.8)"  "0.0 - 210.7 (23.8)"
[1] "hr=" "3.9"
D78V2, continuous
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     5   2   2   0
  20Q LOSS WILD-TYPE 130  68  19   8
D78V3, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                5                130
  T2                2                 68
  T3                2                 19
  T4                0                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V4, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   0
  20Q LOSS WILD-TYPE 124  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    0
  20Q LOSS WILD-TYPE  124   56
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                5                124
  1                0                 56
[1] 2 2
[1] FALSE
D78V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   1
  20Q LOSS WILD-TYPE 105   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    1
  20Q LOSS WILD-TYPE  105    9
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                3                105
  1                1                  9
[1] 2 2
[1] FALSE
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   6
  20Q LOSS WILD-TYPE  52 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    6
  20Q LOSS WILD-TYPE   52  117
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 3                 52
  YES                6                117
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED               0                                9
  20Q LOSS WILD-TYPE             6                              233
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20Q LOSS MUTATED                                               0
  20Q LOSS WILD-TYPE                                             6
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20Q LOSS MUTATED                                     0
  20Q LOSS WILD-TYPE                                  21
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20Q LOSS MUTATED                                           0
  20Q LOSS WILD-TYPE                                         3
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20Q LOSS MUTATED                                              1
  20Q LOSS WILD-TYPE                                           16
D78V7, multiclass
                                               clus
vv                                              20Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             9
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              20Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  6
  CERVICAL SQUAMOUS CELL CARCINOMA                             233
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  6
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           21
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V8, continuous
D78V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  1     0
  20Q LOSS WILD-TYPE                                7    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q LOSS MUTATED                           0
  20Q LOSS WILD-TYPE                        28
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q LOSS MUTATED                                           0     9
  20Q LOSS WILD-TYPE                                         2   193
D78V10, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                0                 28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                    9                193
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V11, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   3
  20Q LOSS WILD-TYPE  23 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    3
  20Q LOSS WILD-TYPE   23  159
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 23
  NOT HISPANIC OR LATINO                3                159
[1] 2 2
[1] FALSE
D78V12, continuous
D78V13, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4   6
  20Q LOSS WILD-TYPE 179  68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    6
  20Q LOSS WILD-TYPE  179   68
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  TUMOR FREE                4                179
  WITH TUMOR                6                 68
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  20Q LOSS MUTATED     0   5   2   0   2
  20Q LOSS WILD-TYPE  18 124 113   1  22
D78V14, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  G1                0                 18
  G2                5                124
  G3                2                113
  G4                0                  1
  GX                2                 22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V15, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 42 
        TCGA-2W-A8YY         TCGA-BI-A0VR         TCGA-C5-A1BJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BQ         TCGA-C5-A1ME 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A2M2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A7CM         TCGA-C5-A7CO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A907         TCGA-DG-A2KK         TCGA-DS-A3LQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EK-A2RA         TCGA-EX-A69M         TCGA-FU-A2QG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-HM-A3JK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JX-A3Q0         TCGA-MA-AA43 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-VS-A8QF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A94Z         TCGA-VS-A9V0         TCGA-VS-A9V4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-WL-A834         TCGA-ZJ-A8QR         TCGA-ZJ-AAX4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-ZJ-AAXA         TCGA-ZJ-AAXT         TCGA-ZJ-AB0I 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D78V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20Q LOSS MUTATED                                             1
  20Q LOSS WILD-TYPE                                          37
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  20Q LOSS MUTATED                                        0
  20Q LOSS WILD-TYPE                                      9
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  20Q LOSS MUTATED                                                 0
  20Q LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20Q LOSS MUTATED                5                   3
  20Q LOSS WILD-TYPE             57                 140
D78V17, multiclass
                                                 clus
vv                                                20Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 5
  LIFELONG NON-SMOKER                                            3
                                                 clus
vv                                                20Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     37
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  57
  LIFELONG NON-SMOKER                                            140
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V18, continuous
D78V19, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    0  0
  20Q LOSS WILD-TYPE 25  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    0
  20Q LOSS WILD-TYPE   25    3
D78V20, continuous
D78V21, continuous
D78V22, continuous
D78V23, continuous
D78V24, continuous
D78V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  20Q LOSS MUTATED                                     0
  20Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  20Q LOSS MUTATED                                     0
  20Q LOSS WILD-TYPE                                   7
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  20Q LOSS MUTATED                         2                       0
  20Q LOSS WILD-TYPE                      34                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20Q LOSS MUTATED                         0
  20Q LOSS WILD-TYPE                       8
D78V26, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 53 
        TCGA-2W-A8YY         TCGA-BI-A20A         TCGA-C5-A0TN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BE         TCGA-C5-A1BK         TCGA-C5-A1BM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M7         TCGA-C5-A1M8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M9         TCGA-C5-A1ME         TCGA-C5-A1MF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MJ         TCGA-C5-A1MP         TCGA-C5-A2LS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LV         TCGA-C5-A2LX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A3HE         TCGA-C5-A3HL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CJ         TCGA-C5-A7UC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7UI         TCGA-C5-A7X8         TCGA-C5-A7XC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A8XI         TCGA-DG-A2KK         TCGA-DG-A2KL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EK-A2RN         TCGA-EK-A2RO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A51Y         TCGA-MU-A8JM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-VS-A8QA         TCGA-VS-A9UT         TCGA-WL-A834 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-XS-A8TJ         TCGA-ZJ-AAX4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  20Q LOSS MUTATED                                               0
  20Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  20Q LOSS MUTATED                                                2
  20Q LOSS WILD-TYPE                                             23
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20Q LOSS MUTATED                                                                                   0
  20Q LOSS WILD-TYPE                                                                                82
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20Q LOSS MUTATED                                                                                              6
  20Q LOSS WILD-TYPE                                                                                          115
D78V27, multiclass
                                                                                              clus
vv                                                                                             20Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              2
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           0
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                6
                                                                                              clus
vv                                                                                             20Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               23
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            82
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V28, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  2
  20Q LOSS WILD-TYPE 70 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE   70   72
         clus
vv        20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ABSENT                 1                 70
  PRESENT                2                 72
[1] 2 2
[1] FALSE
D78V29, continuous
D78V30, continuous
D78V31, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   1
  20Q LOSS WILD-TYPE  46 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    1
  20Q LOSS WILD-TYPE   46  116
                                          clus
vv                                         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 46
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                1                116
[1] 2 2
[1] FALSE
D78V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20Q LOSS MUTATED              1           1          5
  20Q LOSS WILD-TYPE           14          53         80
D78V33, multiclass
              clus
vv             20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CURRENT USER                1                 14
  FORMER USER                 1                 53
  NEVER USED                  5                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V34, continuous
D78V35, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  1
  20Q LOSS WILD-TYPE 91 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    1
  20Q LOSS WILD-TYPE   91   17
         clus
vv        20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ABSENT                 1                 91
  PRESENT                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  20Q LOSS MUTATED             0         3     0
  20Q LOSS WILD-TYPE           5        97     2
D78V36, multiclass
             clus
vv            20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                  3                 97
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V37, continuous
D78V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  20Q LOSS MUTATED         0        0         0         0        1         3
  20Q LOSS WILD-TYPE       5        1         1         1       33        74
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  20Q LOSS MUTATED           1        0         0          0          0
  20Q LOSS WILD-TYPE        36        4         8          5          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  20Q LOSS MUTATED           2         0          0          2         0
  20Q LOSS WILD-TYPE        42         1          3         40         7
                    vv
clus                 STAGE IVB
  20Q LOSS MUTATED           1
  20Q LOSS WILD-TYPE        11
D78V39, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  1                 33
  STAGE IB1                 3                 74
  STAGE IB2                 1                 36
  STAGE II                  0                  4
  STAGE IIA                 0                  8
  STAGE IIA1                0                  5
  STAGE IIA2                0                  7
  STAGE IIB                 2                 42
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB                2                 40
  STAGE IVA                 0                  7
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    32  15
  21Q LOSS WILD-TYPE 179  52
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                47                231 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 52 
$`21Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A2LT 
       57.04        23.67        11.44        35.01         0.46        73.18 
TCGA-C5-A2LV TCGA-C5-A7X3 TCGA-C5-A8XH TCGA-C5-A8YQ TCGA-C5-A8YR TCGA-DG-A2KJ 
       73.45         9.34        45.83        23.51        27.52        95.11 
TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A556 
       87.75        55.63        30.90        24.56        31.73        14.89 
TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PK TCGA-EK-A2R8 TCGA-EK-A2RL 
        0.36        12.59         1.51         0.39         1.45        47.77 
TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3NI TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-JW-A5VG 
       15.22        23.84        20.98        21.67         9.44        27.42 
TCGA-LP-A7HU TCGA-PN-A8MA TCGA-UC-A7PG TCGA-VS-A8EB TCGA-VS-A8EH TCGA-VS-A8EI 
       13.35         2.96        12.16        10.03        32.42        23.97 
TCGA-VS-A8Q9 TCGA-VS-A94Y TCGA-VS-A950 TCGA-VS-A957 TCGA-VS-A959 TCGA-VS-A9U5 
       53.59         4.73        40.14        55.50        51.32        50.47 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UL TCGA-VS-A9UP TCGA-ZJ-A8QR 
       24.30        46.92        14.53        47.47        19.13 

$`21Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       17.52        17.82        49.48        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        31.40        46.32        30.21        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML TCGA-C5-A1MN TCGA-C5-A1MP 
       38.99        35.61         2.43        20.91        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        83.05        78.35       100.14        38.43        33.24 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       52.01        18.02        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48        20.35       147.35        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC 
      155.77       131.11        94.95        13.61         2.73        50.99 
TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
        8.35       146.86        99.91        20.81        20.91        14.73 
TCGA-DG-A2KH TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZM TCGA-DS-A0VK 
        1.12        82.06        44.94        63.98        58.88        36.76 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
       69.96        95.67        22.98        16.83        16.18        17.52 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28        39.55        40.87        37.35        31.53        31.36 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S 
       13.05        25.02        36.89        26.40        26.01         0.30 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       24.82         7.46        26.79        25.91        27.29        27.25 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP 
       27.22        24.00        13.48        60.72        26.27         6.64 
TCGA-EK-A2PI TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R9 TCGA-EK-A2RA 
       19.27         0.43         0.59         0.36         0.13        40.96 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK 
        4.31         0.10         0.43         0.53         0.10         0.49 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L 
        0.76         0.03        20.35         7.92        14.70        19.79 
TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        8.32        15.55         1.22        19.04        16.11        31.36 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       36.26        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC 
       35.44        10.55         1.12        17.75        25.41        16.57 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       20.78        14.93       147.39       137.16        66.81       129.37 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VH 
       96.95        78.71        81.96        29.85        36.36         3.29 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       24.56        21.44        20.48        15.58        28.37         8.28 
TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 TCGA-JX-A5QV TCGA-LP-A4AU 
       18.15        21.11       209.59        44.61        20.91        11.28 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3W TCGA-MA-AA3X 
        0.89        12.49         0.30         0.82        22.52        19.56 
TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y 
       17.82        19.56         8.35         8.52        11.38        28.08 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-MY-A913 
       34.62        19.96        54.81        35.05        20.84        17.23 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
       15.58        16.41        15.95         9.04        16.14        17.56 
TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S TCGA-R2-A69V 
       14.07        15.88         9.34        18.64        22.62        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EC TCGA-VS-A8EG 
       14.60        11.67        93.99        69.50        46.52        45.57 
TCGA-VS-A8EJ TCGA-VS-A8EL TCGA-VS-A8Q8 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       19.96        65.49        32.15        36.13        11.51        59.18 
TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 
       39.78        31.27        40.87        16.64        33.37        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A958 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA 
       15.68        56.35        50.14        43.40        48.39        28.50 
TCGA-VS-A9UB TCGA-VS-A9UC TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UM TCGA-VS-A9UO 
       29.95        27.12        45.11         1.71        27.25        47.87 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       41.52        26.07        15.85        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 
       67.20        18.84         5.16        18.25        17.75         4.34 
TCGA-VS-A9V5 TCGA-VS-AA62 TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 
       16.24        15.42        26.01        29.26        67.59         0.69 
TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
        1.41         0.16         3.91 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.36               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             95.11             210.67 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             23.97              21.44 
[1] "0.4 - 95.1 (24.0)"  "0.0 - 210.7 (21.4)"
[1] "hr=" "1.5"
D79V2, continuous
                    vv
clus                  T1  T2  T3  T4
  21Q LOSS MUTATED    21  12   8   1
  21Q LOSS WILD-TYPE 114  58  13   7
D79V3, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               21                114
  T2               12                 58
  T3                8                 13
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V4, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    20   9
  21Q LOSS WILD-TYPE 109  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     20    9
  21Q LOSS WILD-TYPE  109   47
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               20                109
  1                9                 47
[1] 2 2
[1] FALSE
D79V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   19  2
  21Q LOSS WILD-TYPE 89  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     19    2
  21Q LOSS WILD-TYPE   89    8
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               19                 89
  1                2                  8
[1] 2 2
[1] FALSE
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     6  20
  21Q LOSS WILD-TYPE  49 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6   20
  21Q LOSS WILD-TYPE   49  103
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 6                 49
  YES               20                103
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED               1                               41
  21Q LOSS WILD-TYPE             5                              201
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  21Q LOSS MUTATED                                               1
  21Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  21Q LOSS MUTATED                                     4
  21Q LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  21Q LOSS MUTATED                                           1
  21Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  21Q LOSS MUTATED                                              1
  21Q LOSS WILD-TYPE                                           16
D79V7, multiclass
                                               clus
vv                                              21Q LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            41
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              21Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             201
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  16
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V8, continuous
D79V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     3
  21Q LOSS WILD-TYPE                                7    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED                           9
  21Q LOSS WILD-TYPE                        19
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           1    30
  21Q LOSS WILD-TYPE                                         1   172
D79V10, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  7
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                9                 19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  1
  WHITE                                                   30                172
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V11, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  29
  21Q LOSS WILD-TYPE  22 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   29
  21Q LOSS WILD-TYPE   22  133
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 22
  NOT HISPANIC OR LATINO               29                133
[1] 2 2
[1] FALSE
D79V12, continuous
D79V13, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    29  14
  21Q LOSS WILD-TYPE 154  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     29   14
  21Q LOSS WILD-TYPE  154   60
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  TUMOR FREE               29                154
  WITH TUMOR               14                 60
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  21Q LOSS MUTATED     1  13  29   0   5
  21Q LOSS WILD-TYPE  17 116  86   1  19
D79V14, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  G1                1                 17
  G2               13                116
  G3               29                 86
  G4                0                  1
  GX                5                 19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V15, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 41 
        TCGA-2W-A8YY         TCGA-BI-A0VR         TCGA-C5-A1BJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BQ         TCGA-C5-A1ME 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A2M2 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A7CM         TCGA-C5-A7CO 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A907         TCGA-DG-A2KK         TCGA-DS-A3LQ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EK-A2RA         TCGA-EX-A69M         TCGA-FU-A2QG 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-HM-A3JK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JX-A3Q0         TCGA-MA-AA43 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-Q1-A73S         TCGA-RA-A741         TCGA-VS-A8QF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-VS-A94Z         TCGA-VS-A9V0         TCGA-VS-A9V4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-WL-A834         TCGA-ZJ-AAX4         TCGA-ZJ-AAXA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ZJ-AAXT         TCGA-ZJ-AB0I 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D79V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  21Q LOSS MUTATED                                             1
  21Q LOSS WILD-TYPE                                          37
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  21Q LOSS MUTATED                                        0
  21Q LOSS WILD-TYPE                                      9
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  21Q LOSS MUTATED                                                 0
  21Q LOSS WILD-TYPE                                               3
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  21Q LOSS MUTATED               13                  25
  21Q LOSS WILD-TYPE             49                 118
D79V17, multiclass
                                                 clus
vv                                                21Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                13
  LIFELONG NON-SMOKER                                           25
                                                 clus
vv                                                21Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     37
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           9
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  3
  CURRENT SMOKER                                                  49
  LIFELONG NON-SMOKER                                            118
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V18, continuous
D79V19, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    3  1
  21Q LOSS WILD-TYPE 22  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    1
  21Q LOSS WILD-TYPE   22    2
                         clus
vv                        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   3                 22
  TREATMENT NOT COMPLETED                1                  2
[1] 2 2
[1] FALSE
D79V20, continuous
D79V21, continuous
D79V22, continuous
D79V23, continuous
D79V24, continuous
D79V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  21Q LOSS MUTATED                                     0
  21Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  21Q LOSS MUTATED                                     2
  21Q LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  21Q LOSS MUTATED                         6                       0
  21Q LOSS WILD-TYPE                      30                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  21Q LOSS MUTATED                         0
  21Q LOSS WILD-TYPE                       8
D79V26, multiclass
                                     clus
vv                                    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  5
  OTHER LOCATION, SPECIFY                            6                 30
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  21Q LOSS MUTATED                                               0
  21Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  21Q LOSS MUTATED                                                3
  21Q LOSS WILD-TYPE                                             22
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  21Q LOSS MUTATED                                                                                  14
  21Q LOSS WILD-TYPE                                                                                68
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  21Q LOSS MUTATED                                                                                             22
  21Q LOSS WILD-TYPE                                                                                           99
D79V27, multiclass
                                                                                              clus
vv                                                                                             21Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               0
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               22
                                                                                              clus
vv                                                                                             21Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V28, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   12 11
  21Q LOSS WILD-TYPE 59 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     12   11
  21Q LOSS WILD-TYPE   59   63
         clus
vv        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ABSENT                12                 59
  PRESENT               11                 63
[1] 2 2
[1] FALSE
D79V29, continuous
D79V30, continuous
D79V31, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    7 20
  21Q LOSS WILD-TYPE 42 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7   20
  21Q LOSS WILD-TYPE   42   97
                                          clus
vv                                         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    7                 42
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               20                 97
[1] 2 2
[1] FALSE
D79V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  21Q LOSS MUTATED              3           5         20
  21Q LOSS WILD-TYPE           12          49         65
D79V33, multiclass
              clus
vv             21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CURRENT USER                3                 12
  FORMER USER                 5                 49
  NEVER USED                 20                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V34, continuous
D79V35, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   15  4
  21Q LOSS WILD-TYPE 77 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     15    4
  21Q LOSS WILD-TYPE   77   14
         clus
vv        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ABSENT                15                 77
  PRESENT                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  21Q LOSS MUTATED             0        17     0
  21Q LOSS WILD-TYPE           5        83     2
D79V36, multiclass
             clus
vv            21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 17                 83
  OTHER                      0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V37, continuous
D79V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  21Q LOSS MUTATED         1        0         0         0        7        12
  21Q LOSS WILD-TYPE       4        1         1         1       27        65
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  21Q LOSS MUTATED           5        2         2          3          0
  21Q LOSS WILD-TYPE        32        2         6          2          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  21Q LOSS MUTATED           5         0          2          7         1
  21Q LOSS WILD-TYPE        39         1          1         35         6
                    vv
clus                 STAGE IVB
  21Q LOSS MUTATED           1
  21Q LOSS WILD-TYPE        11
D79V39, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                  7                 27
  STAGE IB1                12                 65
  STAGE IB2                 5                 32
  STAGE II                  2                  2
  STAGE IIA                 2                  6
  STAGE IIA1                3                  2
  STAGE IIA2                0                  7
  STAGE IIB                 5                 39
  STAGE III                 0                  1
  STAGE IIIA                2                  1
  STAGE IIIB                7                 35
  STAGE IVA                 1                  6
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    49  19
  22Q LOSS WILD-TYPE 162  48
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                68                210 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                19                 48 
$`22Q LOSS MUTATED`
TCGA-4J-AA1J TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 
       17.82        23.67        18.74       173.29         5.46        31.40 
TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD 
       30.21        57.73         0.46        73.18        83.05        52.01 
TCGA-C5-A3HE TCGA-C5-A7CM TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-C5-A8YR TCGA-DG-A2KH 
       18.02        20.35         9.34         2.73        27.52         1.12 
TCGA-DG-A2KJ TCGA-DG-A2KL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 
       95.11        44.94        95.67        40.87        30.90        24.56 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2PK 
       31.73         0.30         0.36        12.59         1.51         0.39 
TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2RN TCGA-EK-A3GM TCGA-EX-A8YF TCGA-HM-A3JJ 
        0.36         1.45         0.53         0.76        15.55        21.67 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-JW-A5VG TCGA-JX-A5QV TCGA-LP-A7HU 
      137.16        66.81       129.37        27.42        20.91        13.35 
TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MY-A913 TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       22.52        19.56        17.23        15.58        16.41         9.04 
TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PG TCGA-VS-A8EC TCGA-VS-A8EI TCGA-VS-A8EJ 
       19.59        11.67        12.16        46.52        23.97        19.96 
TCGA-VS-A8EL TCGA-VS-A8QH TCGA-VS-A94X TCGA-VS-A94Y TCGA-VS-A952 TCGA-VS-A953 
       65.49        39.78        16.64         4.73        58.45        15.68 
TCGA-VS-A957 TCGA-VS-A9UI TCGA-VS-A9UL TCGA-VS-A9UM TCGA-VS-A9UT TCGA-XS-A8TJ 
       55.50        45.11        14.53        27.25        15.85        29.26 
TCGA-ZJ-AAX4 TCGA-ZJ-AAXA 
        0.69         1.41 

$`22Q LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI 
       17.52        49.48        57.04        11.44        68.84        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 
      144.16       177.04        82.85        19.86        67.46        46.32 
TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1ML 
       35.01        53.16        38.99        35.61         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ 
       40.93         3.58        44.22        73.45        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       38.43        33.24        17.85        20.42       210.67       154.32 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48       147.35        17.19       155.77 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI 
      131.11        94.95        13.61        50.99        45.83         8.35 
TCGA-C5-A8XJ TCGA-C5-A8XK TCGA-C5-A8YQ TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 
      146.86        99.91        23.51        20.81        20.91        14.73 
TCGA-DG-A2KK TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       82.06        63.98        87.75        58.88        36.76        55.63 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       69.96        22.98        16.83        16.18        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       39.55        37.35        31.53        31.36        13.05        25.02 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       36.89        26.40        26.01        24.82         7.46        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI TCGA-EK-A2PL 
       13.48        60.72        26.27         6.64        19.27         0.43 
TCGA-EK-A2PM TCGA-EK-A2R9 TCGA-EK-A2RA TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RK 
        0.59         0.13        40.96         4.31         0.10         0.43 
TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
       47.77         0.10         0.49         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
       15.22        14.70        19.79         8.32         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       19.04        16.11        31.36        36.26        20.98        26.14 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48        16.14        28.31        14.01        35.44        10.55 
TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JK TCGA-HM-A4S6 
        1.12        17.75        25.41        16.57        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
        9.44       147.39        96.95        78.71        81.96        29.85 
TCGA-IR-A3LL TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36         3.29        24.56        21.44        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH TCGA-JX-A3PZ TCGA-JX-A3Q0 TCGA-JX-A3Q8 
       28.37         8.28        18.15        21.11       209.59        44.61 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 TCGA-MA-AA3Y 
       11.28         0.89        12.49         0.30         0.82        17.82 
TCGA-MA-AA3Z TCGA-MA-AA41 TCGA-MA-AA42 TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI 
       19.56         8.35         8.52        11.38        28.08        34.62 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R3 
       19.96        54.81        35.05        20.84         2.96        15.95 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-RA-A741 TCGA-UC-A7PF TCGA-UC-A7PI TCGA-VS-A8EB TCGA-VS-A8EG 
       22.62        14.60        93.99        69.50        10.03        45.57 
TCGA-VS-A8EH TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF 
       32.42        32.15        53.59        36.13        11.51        59.18 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A954 TCGA-VS-A958 
       31.27        40.87        33.37        40.14        56.35        50.14 
TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UA TCGA-VS-A9UB 
       51.32        50.47        43.40        48.39        28.50        29.95 
TCGA-VS-A9UC TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UJ TCGA-VS-A9UO TCGA-VS-A9UP 
       27.12        24.30        46.92         1.71        47.87        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UR TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ 
       41.52        26.07        14.53         3.42        18.25        67.20 
TCGA-VS-A9V0 TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-A9V5 
       18.84         5.16        18.25        17.75         4.34        16.24 
TCGA-VS-AA62 TCGA-WL-A834 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       15.42        26.01        67.59        19.13         0.16         3.91 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.30               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            173.29             210.67 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            19.775             24.690 
[1] "0.3 - 173.3 (19.8)" "0.0 - 210.7 (24.7)"
[1] "hr=" "1.4"
D80V2, continuous
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED    31  16   8   1
  22Q LOSS WILD-TYPE 104  54  13   7
D80V3, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               31                104
  T2               16                 54
  T3                8                 13
  T4                1                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V4, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   32 13
  22Q LOSS WILD-TYPE 97 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     32   13
  22Q LOSS WILD-TYPE   97   43
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               32                 97
  1               13                 43
[1] 2 2
[1] FALSE
D80V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   34  2
  22Q LOSS WILD-TYPE 74  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     34    2
  22Q LOSS WILD-TYPE   74    8
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               34                 74
  1                2                  8
[1] 2 2
[1] FALSE
D80V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    9 33
  22Q LOSS WILD-TYPE 46 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   33
  22Q LOSS WILD-TYPE   46   90
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 9                 46
  YES               33                 90
[1] 2 2
[1] FALSE
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED               1                               58
  22Q LOSS WILD-TYPE             5                              184
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  22Q LOSS MUTATED                                               1
  22Q LOSS WILD-TYPE                                             5
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  22Q LOSS MUTATED                                     5
  22Q LOSS WILD-TYPE                                  16
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  22Q LOSS MUTATED                                           1
  22Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  22Q LOSS MUTATED                                              5
  22Q LOSS WILD-TYPE                                           12
D80V7, multiclass
                                               clus
vv                                              22Q LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            58
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 5
                                               clus
vv                                              22Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  5
  CERVICAL SQUAMOUS CELL CARCINOMA                             184
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V8, continuous
D80V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  2     3
  22Q LOSS WILD-TYPE                                6    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED                           9
  22Q LOSS WILD-TYPE                        19
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           0    51
  22Q LOSS WILD-TYPE                                         2   151
D80V10, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  6
  ASIAN                                                    3                 16
  BLACK OR AFRICAN AMERICAN                                9                 19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  2
  WHITE                                                   51                151
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     6  36
  22Q LOSS WILD-TYPE  17 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   36
  22Q LOSS WILD-TYPE   17  126
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 17
  NOT HISPANIC OR LATINO               36                126
[1] 2 2
[1] FALSE
D80V12, continuous
D80V13, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    41  17
  22Q LOSS WILD-TYPE 142  57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     41   17
  22Q LOSS WILD-TYPE  142   57
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  TUMOR FREE               41                142
  WITH TUMOR               17                 57
[1] 2 2
[1] FALSE
                    vv
clus                  G1  G2  G3  G4  GX
  22Q LOSS MUTATED     4  28  32   0   6
  22Q LOSS WILD-TYPE  14 101  83   1  18
D80V14, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  G1                4                 14
  G2               28                101
  G3               32                 83
  G4                0                  1
  GX                6                 18
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V15, continuous
D80V16, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  22Q LOSS MUTATED                                             6
  22Q LOSS WILD-TYPE                                          32
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  22Q LOSS MUTATED                                        2
  22Q LOSS WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  22Q LOSS MUTATED                                                 2
  22Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  22Q LOSS MUTATED               11                  37
  22Q LOSS WILD-TYPE             51                 106
D80V17, multiclass
                                                 clus
vv                                                22Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                2
  CURRENT SMOKER                                                11
  LIFELONG NON-SMOKER                                           37
                                                 clus
vv                                                22Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     32
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  51
  LIFELONG NON-SMOKER                                            106
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V18, continuous
D80V19, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    9  0
  22Q LOSS WILD-TYPE 16  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9    0
  22Q LOSS WILD-TYPE   16    3
                         clus
vv                        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COMPLETED AS PLANNED                   9                 16
  TREATMENT NOT COMPLETED                0                  3
[1] 2 2
[1] FALSE
D80V20, continuous
D80V21, continuous
D80V22, continuous
D80V23, continuous
D80V24, continuous
D80V25, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  22Q LOSS MUTATED                                     0
  22Q LOSS WILD-TYPE                                   3
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  22Q LOSS MUTATED                                     1
  22Q LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  22Q LOSS MUTATED                        11                       0
  22Q LOSS WILD-TYPE                      25                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  22Q LOSS MUTATED                         3
  22Q LOSS WILD-TYPE                       5
D80V26, multiclass
                                     clus
vv                                    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  6
  OTHER LOCATION, SPECIFY                           11                 25
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  22Q LOSS MUTATED                                               1
  22Q LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  22Q LOSS MUTATED                                                3
  22Q LOSS WILD-TYPE                                             22
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  22Q LOSS MUTATED                                                                                  26
  22Q LOSS WILD-TYPE                                                                                56
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  22Q LOSS MUTATED                                                                                             25
  22Q LOSS WILD-TYPE                                                                                           96
D80V27, multiclass
                                                                                              clus
vv                                                                                             22Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              3
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                          26
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               25
                                                                                              clus
vv                                                                                             22Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               22
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            56
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V28, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   17 22
  22Q LOSS WILD-TYPE 54 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     17   22
  22Q LOSS WILD-TYPE   54   52
         clus
vv        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ABSENT                17                 54
  PRESENT               22                 52
[1] 2 2
[1] FALSE
D80V29, continuous
D80V30, continuous
D80V31, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    9 31
  22Q LOSS WILD-TYPE 40 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   31
  22Q LOSS WILD-TYPE   40   86
                                          clus
vv                                         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 40
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               31                 86
[1] 2 2
[1] FALSE
D80V32, continuous
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  22Q LOSS MUTATED              5          12         23
  22Q LOSS WILD-TYPE           10          42         62
D80V33, multiclass
              clus
vv             22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CURRENT USER                5                 10
  FORMER USER                12                 42
  NEVER USED                 23                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V34, continuous
D80V35, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   26  3
  22Q LOSS WILD-TYPE 66 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     26    3
  22Q LOSS WILD-TYPE   66   15
         clus
vv        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ABSENT                26                 66
  PRESENT                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CARBOPLATIN CISPLATIN OTHER
  22Q LOSS MUTATED             0        26     1
  22Q LOSS WILD-TYPE           5        74     1
D80V36, multiclass
             clus
vv            22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CARBOPLATIN                0                  5
  CISPLATIN                 26                 74
  OTHER                      1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V37, continuous
D80V38, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  22Q LOSS MUTATED         1        0         0         0       10        23
  22Q LOSS WILD-TYPE       4        1         1         1       24        54
                    vv
clus                 STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  22Q LOSS MUTATED           7        3         4          1          0
  22Q LOSS WILD-TYPE        30        1         4          4          7
                    vv
clus                 STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  22Q LOSS MUTATED           8         0          0         10         1
  22Q LOSS WILD-TYPE        36         1          3         32         6
                    vv
clus                 STAGE IVB
  22Q LOSS MUTATED           1
  22Q LOSS WILD-TYPE        11
D80V39, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                  0                  1
  STAGE IA1                 0                  1
  STAGE IA2                 0                  1
  STAGE IB                 10                 24
  STAGE IB1                23                 54
  STAGE IB2                 7                 30
  STAGE II                  3                  1
  STAGE IIA                 4                  4
  STAGE IIA1                1                  4
  STAGE IIA2                0                  7
  STAGE IIB                 8                 36
  STAGE III                 0                  1
  STAGE IIIA                0                  3
  STAGE IIIB               10                 32
  STAGE IVA                 1                  6
  STAGE IVB                 1                 11
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    43  15
  XP LOSS WILD-TYPE 168  52
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               58               220 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               15                52 
$`XP LOSS MUTATED`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1ML 
       57.04        23.67        11.44        30.21        53.16        20.91 
TCGA-C5-A1MN TCGA-C5-A2LV TCGA-C5-A3HD TCGA-C5-A7CJ TCGA-C5-A7UH TCGA-C5-A8XK 
       40.93        73.45        52.01       101.82       131.11        99.91 
TCGA-C5-A8YQ TCGA-DS-A0VN TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A43B 
       23.51        95.67        16.18        40.87        25.02        26.01 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2PL TCGA-EK-A2PM 
        0.30        14.89        60.72         1.51         0.43         0.59 
TCGA-EK-A2RA TCGA-EK-A2RK TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
       40.96         0.43         0.10         0.49        20.35         7.92 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A5XV TCGA-IR-A3LA TCGA-IR-A3LB 
       19.04        31.36        20.98        10.55       137.16        66.81 
TCGA-IR-A3LK TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-MA-AA42 TCGA-MY-A5BF 
       29.85        21.11        44.61         0.89         8.52        20.84 
TCGA-UC-A7PI TCGA-VS-A8EH TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A94Y TCGA-VS-A950 
       69.50        32.42        11.51        59.18         4.73        40.14 
TCGA-VS-A9U7 TCGA-VS-A9UC TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UR TCGA-VS-A9UT 
       48.39        27.12        27.25        47.87        26.07        15.85 
TCGA-VS-A9V5 TCGA-ZJ-A8QQ TCGA-ZJ-A8QR TCGA-ZJ-AAX4 
       16.24        67.59        19.13         0.69 

$`XP LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       17.52        17.82        49.48        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
      144.16       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MH 
       67.46        31.40        46.32        35.01        57.73        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       35.61         0.46         2.43         3.58        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE 
       83.05        78.35       100.14        38.43        33.24        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       210.67       154.32       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
       20.35       147.35        17.19       155.77        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ 
       13.61         2.73        50.99        45.83         8.35       146.86 
TCGA-C5-A8YR TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ 
       27.52        20.81        20.91        14.73         1.12        95.11 
TCGA-DG-A2KK TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       82.06        44.94        63.98        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI 
       55.63        69.96        22.98        16.83        17.52         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       39.55        37.35        30.90        31.53        31.36        13.05 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A50E 
       36.89        26.40        24.56        31.73        24.82         7.46 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
       26.79        25.91        27.29        27.25        27.22        24.00 
TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PI 
       13.48         0.36        12.59        26.27         6.64        19.27 
TCGA-EK-A2PK TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RD 
        0.39         0.36         1.45         0.13         4.31         0.10 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A449 
       47.77         0.53         0.76         0.03        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
       19.79         8.32        15.55         1.22        23.84        16.11 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       36.26        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44         1.12        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC TCGA-IR-A3LF 
       20.78        14.93         9.44       147.39       129.37        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VH TCGA-JW-A5VI 
       78.71        81.96        36.36        27.42         3.29        24.56 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-JW-AAVH 
       21.44        20.48        15.58        28.37         8.28        18.15 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
      209.59        20.91        11.28        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA41 
       13.35        22.52        19.56        17.82        19.56         8.35 
TCGA-MA-AA43 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
       11.38        28.08        34.62        19.96        54.81        35.05 
TCGA-MY-A913 TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       17.23         2.96        15.58        16.41        15.95         9.04 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R 
       16.14        17.56        14.07        15.88         9.34        18.64 
TCGA-Q1-A73S TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG 
       22.62        19.59        14.60        11.67        93.99        12.16 
TCGA-VS-A8EB TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       10.03        46.52        45.57        23.97        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QH TCGA-VS-A8QM TCGA-VS-A94W 
       32.15        53.59        36.13        39.78        31.27        40.87 
TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A952 TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 
       16.64        33.37        58.45        15.68        56.35        55.50 
TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 TCGA-VS-A9U6 TCGA-VS-A9UA TCGA-VS-A9UB 
       50.14        51.32        50.47        43.40        28.50        29.95 
TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ TCGA-VS-A9UL TCGA-VS-A9UP 
       24.30        46.92        45.11         1.71        14.53        47.47 
TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY TCGA-VS-A9UZ TCGA-VS-A9V0 
       41.52        14.53         3.42        18.25        67.20        18.84 
TCGA-VS-A9V1 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-AA62 TCGA-WL-A834 
        5.16        18.25        17.75         4.34        15.42        26.01 
TCGA-XS-A8TJ TCGA-ZJ-AAXA TCGA-ZJ-AAXU TCGA-ZX-AA5X 
       29.26         1.41         0.16         3.91 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.10              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           137.16            210.67 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           25.515            22.095 
[1] "0.1 - 137.2 (25.5)" "0.0 - 210.7 (22.1)"
[1] "hr=" "1"  
D81V2, continuous
                   vv
clus                 T1  T2  T3  T4
  XP LOSS MUTATED    31  14   3   0
  XP LOSS WILD-TYPE 104  56  18   8
D81V3, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              31               104
  T2              14                56
  T3               3                18
  T4               0                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V4, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   30 11
  XP LOSS WILD-TYPE 99 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     30   11
  XP LOSS WILD-TYPE   99   45
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              30                99
  1              11                45
[1] 2 2
[1] FALSE
D81V5, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   19  0
  XP LOSS WILD-TYPE 89 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     19    0
  XP LOSS WILD-TYPE   89   10
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              19                89
  1               0                10
[1] 2 2
[1] FALSE
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     9  23
  XP LOSS WILD-TYPE  46 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      9   23
  XP LOSS WILD-TYPE   46  100
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                9                46
  YES              23               100
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  XP LOSS MUTATED               1                               50
  XP LOSS WILD-TYPE             5                              192
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  XP LOSS MUTATED                                               1
  XP LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  XP LOSS MUTATED                                     4
  XP LOSS WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  XP LOSS MUTATED                                           3
  XP LOSS WILD-TYPE                                         0
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  XP LOSS MUTATED                                              4
  XP LOSS WILD-TYPE                                           13
D81V7, multiclass
                                               clus
vv                                              XP LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   3
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                4
                                               clus
vv                                              XP LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            192
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 13
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V8, continuous
D81V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0     3
  XP LOSS WILD-TYPE                                8    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XP LOSS MUTATED                           6
  XP LOSS WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XP LOSS MUTATED                                           2    47
  XP LOSS WILD-TYPE                                         0   155
D81V10, multiclass
                                           clus
vv                                          XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 8
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               6                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 0
  WHITE                                                  47               155
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V11, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     3  37
  XP LOSS WILD-TYPE  20 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      3   37
  XP LOSS WILD-TYPE   20  125
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                20
  NOT HISPANIC OR LATINO              37               125
[1] 2 2
[1] FALSE
D81V12, continuous
D81V13, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    36  17
  XP LOSS WILD-TYPE 147  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     36   17
  XP LOSS WILD-TYPE  147   57
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  TUMOR FREE              36               147
  WITH TUMOR              17                57
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  XP LOSS MUTATED     4  23  30   0   4
  XP LOSS WILD-TYPE  14 106  85   1  20
D81V14, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  G1               4                14
  G2              23               106
  G3              30                85
  G4               0                 1
  GX               4                20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V15, continuous
D81V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  XP LOSS MUTATED                                             7
  XP LOSS WILD-TYPE                                          31
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  XP LOSS MUTATED                                        1
  XP LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  XP LOSS MUTATED                                                 0
  XP LOSS WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  XP LOSS MUTATED               18                  26
  XP LOSS WILD-TYPE             44                 117
D81V17, multiclass
                                                 clus
vv                                                XP LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               18
  LIFELONG NON-SMOKER                                          26
                                                 clus
vv                                                XP LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 44
  LIFELONG NON-SMOKER                                           117
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V18, continuous
D81V19, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    6  2
  XP LOSS WILD-TYPE 19  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      6    2
  XP LOSS WILD-TYPE   19    1
                         clus
vv                        XP LOSS MUTATED XP LOSS WILD-TYPE
  COMPLETED AS PLANNED                  6                19
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
D81V20, continuous
D81V21, continuous
D81V22, continuous
D81V23, continuous
D81V24, continuous
D81V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  XP LOSS MUTATED                                     0
  XP LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  XP LOSS MUTATED                                     4                       6
  XP LOSS WILD-TYPE                                   3                      30
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  XP LOSS MUTATED                         0                       1
  XP LOSS WILD-TYPE                       1                       7
D81V26, multiclass
                                     clus
vv                                    XP LOSS MUTATED XP LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               4                 3
  OTHER LOCATION, SPECIFY                           6                30
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  XP LOSS MUTATED                                               1
  XP LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  XP LOSS MUTATED                                                7
  XP LOSS WILD-TYPE                                             18
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  XP LOSS MUTATED                                                                                  14
  XP LOSS WILD-TYPE                                                                                68
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  XP LOSS MUTATED                                                                                             26
  XP LOSS WILD-TYPE                                                                                           95
D81V27, multiclass
                                                                                              clus
vv                                                                                             XP LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              26
                                                                                              clus
vv                                                                                             XP LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              18
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           68
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V28, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   15 16
  XP LOSS WILD-TYPE 56 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     15   16
  XP LOSS WILD-TYPE   56   58
         clus
vv        XP LOSS MUTATED XP LOSS WILD-TYPE
  ABSENT               15                56
  PRESENT              16                58
[1] 2 2
[1] FALSE
D81V29, continuous
D81V30, continuous
D81V31, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    15  17
  XP LOSS WILD-TYPE  34 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     15   17
  XP LOSS WILD-TYPE   34  100
                                          clus
vv                                         XP LOSS MUTATED XP LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  15                34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              17               100
[1] 2 2
[1] FALSE
D81V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  XP LOSS MUTATED              4           9         24
  XP LOSS WILD-TYPE           11          45         61
D81V33, multiclass
              clus
vv             XP LOSS MUTATED XP LOSS WILD-TYPE
  CURRENT USER               4                11
  FORMER USER                9                45
  NEVER USED                24                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V34, continuous
D81V35, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   20  2
  XP LOSS WILD-TYPE 72 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     20    2
  XP LOSS WILD-TYPE   72   16
         clus
vv        XP LOSS MUTATED XP LOSS WILD-TYPE
  ABSENT               20                72
  PRESENT               2                16
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  XP LOSS MUTATED             1        19     0
  XP LOSS WILD-TYPE           4        81     2
D81V36, multiclass
             clus
vv            XP LOSS MUTATED XP LOSS WILD-TYPE
  CARBOPLATIN               1                 4
  CISPLATIN                19                81
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V37, continuous
D81V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  XP LOSS MUTATED         1        1         0         1        8        15
  XP LOSS WILD-TYPE       4        0         1         0       26        62
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  XP LOSS MUTATED           7        1         3          0          2
  XP LOSS WILD-TYPE        30        3         5          5          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  XP LOSS MUTATED          12         0          1          6         1
  XP LOSS WILD-TYPE        32         1          2         36         6
                   vv
clus                STAGE IVB
  XP LOSS MUTATED           2
  XP LOSS WILD-TYPE        10
D81V39, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 1                 0
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                 8                26
  STAGE IB1               15                62
  STAGE IB2                7                30
  STAGE II                 1                 3
  STAGE IIA                3                 5
  STAGE IIA1               0                 5
  STAGE IIA2               2                 5
  STAGE IIB               12                32
  STAGE III                0                 1
  STAGE IIIA               1                 2
  STAGE IIIB               6                36
  STAGE IVA                1                 6
  STAGE IVB                2                10
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    37  18
  XQ LOSS WILD-TYPE 174  49
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               55               223 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18                49 
$`XQ LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A1MK TCGA-C5-A1ML 
       23.67        11.44        19.86        30.21         2.43        20.91 
TCGA-C5-A1MN TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A7CJ TCGA-C5-A7CO TCGA-C5-A7UH 
       40.93        83.05        52.01       101.82       147.35       131.11 
TCGA-C5-A7X5 TCGA-C5-A8XK TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WF TCGA-EA-A1QT 
       13.61        99.91        36.76        95.67        16.18        40.87 
TCGA-EA-A3QE TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EK-A2PL 
       25.02        26.01         0.30        14.89        27.25         0.43 
TCGA-EK-A2RA TCGA-EK-A2RK TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 
       40.96         0.43         0.10         0.49        20.35         7.92 
TCGA-EX-A69M TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A5XV TCGA-IR-A3LK TCGA-JW-A5VL 
        8.32        19.04        31.36        10.55        29.85        15.58 
TCGA-JW-A852 TCGA-JX-A3PZ TCGA-JX-A3Q8 TCGA-LP-A4AW TCGA-MA-AA41 TCGA-MA-AA42 
        8.28        21.11        44.61         0.89         8.35         8.52 
TCGA-MY-A5BF TCGA-UC-A7PI TCGA-VS-A94Y TCGA-VS-A9U6 TCGA-VS-A9U7 TCGA-VS-A9UC 
       20.84        69.50         4.73        43.40        48.39        27.12 
TCGA-VS-A9UM TCGA-VS-A9UO TCGA-VS-A9UR TCGA-VS-A9UT TCGA-VS-A9V1 TCGA-VS-A9V5 
       27.25        47.87        26.07        15.85         5.16        16.24 
TCGA-ZJ-A8QR 
       19.13 

$`XQ LOSS WILD-TYPE`
TCGA-2W-A8YY TCGA-4J-AA1J TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF 
       17.52        17.82        49.48        57.04        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
       36.56       144.16       177.04       173.29        82.85         5.46 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        31.40        46.32        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       38.99        35.61         0.46         3.58        44.22        73.18 
TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE 
       73.45        78.35       100.14        38.43        33.24        18.02 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       210.67       154.32       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 
       20.35        17.19       155.77        94.95         9.34         2.73 
TCGA-C5-A7XC TCGA-C5-A8XH TCGA-C5-A8XI TCGA-C5-A8XJ TCGA-C5-A8YQ TCGA-C5-A8YR 
       50.99        45.83         8.35       146.86        23.51        27.52 
TCGA-C5-A8YT TCGA-C5-A8ZZ TCGA-C5-A907 TCGA-DG-A2KH TCGA-DG-A2KJ TCGA-DG-A2KK 
       20.81        20.91        14.73         1.12        95.11        82.06 
TCGA-DG-A2KL TCGA-DG-A2KM TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
       44.94        63.98        87.75        58.88        55.63        69.96 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       22.98        16.83        17.52         8.28        39.55        37.35 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 
       30.90        31.53        31.36        13.05        36.89        26.40 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 
       24.56        31.73        24.82         7.46        26.79        25.91 
TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EA-A97N TCGA-EK-A2GZ 
       27.29        27.22        24.00        13.48         0.36        12.59 
TCGA-EK-A2H0 TCGA-EK-A2H1 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK 
       60.72        26.27         6.64         1.51        19.27         0.39 
TCGA-EK-A2PM TCGA-EK-A2R7 TCGA-EK-A2R8 TCGA-EK-A2R9 TCGA-EK-A2RC TCGA-EK-A2RD 
        0.59         0.36         1.45         0.13         4.31         0.10 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A449 
       47.77         0.53         0.76         0.03        15.22        14.70 
TCGA-EX-A69L TCGA-EX-A8YF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HZ 
       19.79        15.55         1.22        23.84        16.11        36.26 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
       20.98        26.14         1.48        16.14        28.31        14.01 
TCGA-FU-A57G TCGA-FU-A770 TCGA-GH-A9DA TCGA-HG-A2PA TCGA-HG-A9SC TCGA-HM-A3JJ 
       35.44         1.12        17.75        25.41        16.57        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         9.44       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG 
      129.37        96.95        78.71        81.96        36.36        27.42 
TCGA-JW-A5VH TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-JW-AAVH 
        3.29        24.56        21.44        20.48        28.37        18.15 
TCGA-JX-A3Q0 TCGA-JX-A5QV TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U2 TCGA-LP-A5U3 
      209.59        20.91        11.28        12.49         0.30         0.82 
TCGA-LP-A7HU TCGA-MA-AA3W TCGA-MA-AA3X TCGA-MA-AA3Y TCGA-MA-AA3Z TCGA-MA-AA43 
       13.35        22.52        19.56        17.82        19.56        11.38 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A913 
       28.08        34.62        19.96        54.81        35.05        17.23 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96        15.58        16.41        15.95         9.04        16.14 
TCGA-Q1-A6DW TCGA-Q1-A73O TCGA-Q1-A73P TCGA-Q1-A73Q TCGA-Q1-A73R TCGA-Q1-A73S 
       17.56        14.07        15.88         9.34        18.64        22.62 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF TCGA-UC-A7PG TCGA-VS-A8EB 
       19.59        14.60        11.67        93.99        12.16        10.03 
TCGA-VS-A8EC TCGA-VS-A8EG TCGA-VS-A8EH TCGA-VS-A8EI TCGA-VS-A8EJ TCGA-VS-A8EL 
       46.52        45.57        32.42        23.97        19.96        65.49 
TCGA-VS-A8Q8 TCGA-VS-A8Q9 TCGA-VS-A8QA TCGA-VS-A8QC TCGA-VS-A8QF TCGA-VS-A8QH 
       32.15        53.59        36.13        11.51        59.18        39.78 
TCGA-VS-A8QM TCGA-VS-A94W TCGA-VS-A94X TCGA-VS-A94Z TCGA-VS-A950 TCGA-VS-A952 
       31.27        40.87        16.64        33.37        40.14        58.45 
TCGA-VS-A953 TCGA-VS-A954 TCGA-VS-A957 TCGA-VS-A958 TCGA-VS-A959 TCGA-VS-A9U5 
       15.68        56.35        55.50        50.14        51.32        50.47 
TCGA-VS-A9UA TCGA-VS-A9UB TCGA-VS-A9UD TCGA-VS-A9UH TCGA-VS-A9UI TCGA-VS-A9UJ 
       28.50        29.95        24.30        46.92        45.11         1.71 
TCGA-VS-A9UL TCGA-VS-A9UP TCGA-VS-A9UQ TCGA-VS-A9UU TCGA-VS-A9UV TCGA-VS-A9UY 
       14.53        47.47        41.52        14.53         3.42        18.25 
TCGA-VS-A9UZ TCGA-VS-A9V0 TCGA-VS-A9V2 TCGA-VS-A9V3 TCGA-VS-A9V4 TCGA-VS-AA62 
       67.20        18.84        18.25        17.75         4.34        15.42 
TCGA-WL-A834 TCGA-XS-A8TJ TCGA-ZJ-A8QQ TCGA-ZJ-AAX4 TCGA-ZJ-AAXA TCGA-ZJ-AAXU 
       26.01        29.26        67.59         0.69         1.41         0.16 
TCGA-ZX-AA5X 
        3.91 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.10              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           147.35            210.67 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            20.91             23.84 
[1] "0.1 - 147.3 (20.9)" "0.0 - 210.7 (23.8)"
[1] "hr=" "1.6"
D82V2, continuous
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED    28  16   2   1
  XQ LOSS WILD-TYPE 107  54  19   7
D82V3, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              28               107
  T2              16                54
  T3               2                19
  T4               1                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V4, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    26  13
  XQ LOSS WILD-TYPE 103  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     26   13
  XQ LOSS WILD-TYPE  103   43
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              26               103
  1              13                43
[1] 2 2
[1] FALSE
D82V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   16  2
  XQ LOSS WILD-TYPE 92  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     16    2
  XQ LOSS WILD-TYPE   92    8
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              16                92
  1               2                 8
[1] 2 2
[1] FALSE
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    13  21
  XQ LOSS WILD-TYPE  42 102
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13   21
  XQ LOSS WILD-TYPE   42  102
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               13                42
  YES              21               102
[1] 2 2
[1] FALSE
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED               1                               47
  XQ LOSS WILD-TYPE             5                              195
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  XQ LOSS MUTATED                                               1
  XQ LOSS WILD-TYPE                                             5
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  XQ LOSS MUTATED                                     3
  XQ LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  XQ LOSS MUTATED                                           2
  XQ LOSS WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  XQ LOSS MUTATED                                              5
  XQ LOSS WILD-TYPE                                           12
D82V7, multiclass
                                               clus
vv                                              XQ LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           47
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                5
                                               clus
vv                                              XQ LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 5
  CERVICAL SQUAMOUS CELL CARCINOMA                            195
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 5
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 12
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V8, continuous
D82V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  1     4
  XQ LOSS WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED                           5
  XQ LOSS WILD-TYPE                        23
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           2    44
  XQ LOSS WILD-TYPE                                         0   158
D82V10, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 7
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                               5                23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 0
  WHITE                                                  44               158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V11, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     6  35
  XQ LOSS WILD-TYPE  17 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6   35
  XQ LOSS WILD-TYPE   17  127
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                17
  NOT HISPANIC OR LATINO              35               127
[1] 2 2
[1] FALSE
D82V12, continuous
D82V13, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    33  19
  XQ LOSS WILD-TYPE 150  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     33   19
  XQ LOSS WILD-TYPE  150   55
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  TUMOR FREE              33               150
  WITH TUMOR              19                55
[1] 2 2
[1] FALSE
                   vv
clus                 G1  G2  G3  G4  GX
  XQ LOSS MUTATED     5  23  25   0   4
  XQ LOSS WILD-TYPE  13 106  90   1  20
D82V14, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  G1               5                13
  G2              23               106
  G3              25                90
  G4               0                 1
  GX               4                20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V15, continuous
D82V16, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  XQ LOSS MUTATED                                             7
  XQ LOSS WILD-TYPE                                          31
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  XQ LOSS MUTATED                                        1
  XQ LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  XQ LOSS MUTATED                                                 0
  XQ LOSS WILD-TYPE                                               3
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  XQ LOSS MUTATED               13                  29
  XQ LOSS WILD-TYPE             49                 114
D82V17, multiclass
                                                 clus
vv                                                XQ LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               13
  LIFELONG NON-SMOKER                                          29
                                                 clus
vv                                                XQ LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    31
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 3
  CURRENT SMOKER                                                 49
  LIFELONG NON-SMOKER                                           114
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V18, continuous
D82V19, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    6  2
  XQ LOSS WILD-TYPE 19  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6    2
  XQ LOSS WILD-TYPE   19    1
                         clus
vv                        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COMPLETED AS PLANNED                  6                19
  TREATMENT NOT COMPLETED               2                 1
[1] 2 2
[1] FALSE
D82V20, continuous
D82V21, continuous
D82V22, continuous
D82V23, continuous
D82V24, continuous
D82V25, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  XQ LOSS MUTATED                                     0
  XQ LOSS WILD-TYPE                                   3
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  XQ LOSS MUTATED                                     4                       4
  XQ LOSS WILD-TYPE                                   3                      32
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  XQ LOSS MUTATED                         0                       2
  XQ LOSS WILD-TYPE                       1                       6
D82V26, multiclass
                                     clus
vv                                    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 3
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               4                 3
  OTHER LOCATION, SPECIFY                           4                32
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)
  XQ LOSS MUTATED                                               1
  XQ LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  XQ LOSS MUTATED                                                6
  XQ LOSS WILD-TYPE                                             19
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  XQ LOSS MUTATED                                                                                  13
  XQ LOSS WILD-TYPE                                                                                69
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  XQ LOSS MUTATED                                                                                             25
  XQ LOSS WILD-TYPE                                                                                           96
D82V27, multiclass
                                                                                              clus
vv                                                                                             XQ LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                         13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              25
                                                                                              clus
vv                                                                                             XQ LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              19
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           69
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V28, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   14 13
  XQ LOSS WILD-TYPE 57 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     14   13
  XQ LOSS WILD-TYPE   57   61
         clus
vv        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ABSENT               14                57
  PRESENT              13                61
[1] 2 2
[1] FALSE
D82V29, continuous
D82V30, continuous
D82V31, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   17 18
  XQ LOSS WILD-TYPE 32 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     17   18
  XQ LOSS WILD-TYPE   32   99
                                          clus
vv                                         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  17                32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              18                99
[1] 2 2
[1] FALSE
D82V32, continuous
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  XQ LOSS MUTATED              4          11         21
  XQ LOSS WILD-TYPE           11          43         64
D82V33, multiclass
              clus
vv             XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CURRENT USER               4                11
  FORMER USER               11                43
  NEVER USED                21                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V34, continuous
D82V35, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   19  2
  XQ LOSS WILD-TYPE 73 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     19    2
  XQ LOSS WILD-TYPE   73   16
         clus
vv        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ABSENT               19                73
  PRESENT               2                16
[1] 2 2
[1] FALSE
                   vv
clus                CARBOPLATIN CISPLATIN OTHER
  XQ LOSS MUTATED             3        20     0
  XQ LOSS WILD-TYPE           2        80     2
D82V36, multiclass
             clus
vv            XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CARBOPLATIN               3                 2
  CISPLATIN                20                80
  OTHER                     0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V37, continuous
D82V38, continuous
                   vv
clus                STAGE I STAGE IA STAGE IA1 STAGE IA2 STAGE IB STAGE IB1
  XQ LOSS MUTATED         1        1         0         1        7        13
  XQ LOSS WILD-TYPE       4        0         1         0       27        64
                   vv
clus                STAGE IB2 STAGE II STAGE IIA STAGE IIA1 STAGE IIA2
  XQ LOSS MUTATED           9        0         3          0          2
  XQ LOSS WILD-TYPE        28        4         5          5          5
                   vv
clus                STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IVA
  XQ LOSS MUTATED          10         0          0          7         0
  XQ LOSS WILD-TYPE        34         1          3         35         7
                   vv
clus                STAGE IVB
  XQ LOSS MUTATED           4
  XQ LOSS WILD-TYPE         8
D82V39, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 1                 0
  STAGE IA1                0                 1
  STAGE IA2                1                 0
  STAGE IB                 7                27
  STAGE IB1               13                64
  STAGE IB2                9                28
  STAGE II                 0                 4
  STAGE IIA                3                 5
  STAGE IIA1               0                 5
  STAGE IIA2               2                 5
  STAGE IIB               10                34
  STAGE III                0                 1
  STAGE IIIA               0                 3
  STAGE IIIB               7                35
  STAGE IVA                0                 7
  STAGE IVB                4                 8
[1] 17  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
