[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[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/10005797/CESC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CESC-TP/10013687/transformed.cor.cli.txt"

nPatients in clinical file=200, in cluster file=206, common to both=176
[1]  80 176
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               122 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               54               122 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               83                93 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               83                93 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               35               141 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               35               141 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               24               152 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               24               152 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               45               131 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               45               131 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              104                72 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              104                72 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               170 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               170 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               169 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               169 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               61               115 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               61               115 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               29               147 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               29               147 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               35               141 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               35               141 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21               155 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21               155 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               23               153 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               23               153 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22               154 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22               154 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               28               148 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               28               148 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               47               129 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               47               129 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               25               151 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               25               151 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26               150 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26               150 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                162 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                162 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                168 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                168 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                171 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                171 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                171 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                171 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                148 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                148 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                25                151 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                25                151 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                161 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                161 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                26                150 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                26                150 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                30                146 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                30                146 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                24                152 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                24                152 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                21                155 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                21                155 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                164 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                164 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                26                150 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                26                150 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                23                153 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                23                153 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                164 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                164 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                26                150 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                26                150 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                40                136 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                40                136 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                60                116 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                60                116 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                64                112 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                64                112 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                22                154 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                22                154 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                20                156 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                20                156 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               24               152 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               24               152 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7               169 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7               169 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               169 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               169 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               166 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               166 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               160 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               160 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               42               134 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               42               134 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               170 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6               170 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               71               105 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               71               105 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               48               128 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               48               128 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12               164 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               12               164 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               143 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               143 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               24               152 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               24               152 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               42               134 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               42               134 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               17               159 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               17               159 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               26               150 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               26               150 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               49               127 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               49               127 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               161 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               15               161 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               34               142 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               34               142 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29               147 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29               147 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                39                137 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                39                137 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                44                132 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                44                132 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                59                117 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                59                117 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                69                107 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                69                107 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                24                152 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                24                152 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                167 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                167 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                46                130 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                46                130 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                157 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                157 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                24                152 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                24                152 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                20                156 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                20                156 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                26                150 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                26                150 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                52                124 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                52                124 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                159 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                159 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                33                143 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                33                143 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                45                131 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                45                131 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                30                146 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                30                146 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                161 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                161 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                165 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                165 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                172 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                172 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                26                150 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                26                150 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                37                139 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                37                139 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               35               141 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               35               141 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                    
 [2] "VITALSTATUS"                                     
 [3] "DAYSTODEATH"                                     
 [4] "DAYSTOLASTFOLLOWUP"                              
 [5] "PRIMARYSITEOFDESEASE"                            
 [6] "NEOPLASM.DISEASESTAGE"                           
 [7] "PATHOLOGY.T.STAGE"                               
 [8] "PATHOLOGY.N.STAGE"                               
 [9] "PATHOLOGY.M.STAGE"                               
[10] "DCCUPLOADDATE"                                   
[11] "GENDER"                                          
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"                
[13] "HISTOLOGICALTYPE"                                
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"          
[15] "NUMBERPACKYEARSSMOKED"                           
[16] "NUMBER.OF.LYMPH.NODES"                           
[17] "RACE"                                            
[18] "ETHNICITY"                                       
[19] "BATCHNUMBER"                                     
[20] "WEIGHT_KG_AT_DIAGNOSIS"                          
[21] "TUMOR_STATUS"                                    
[22] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[23] "NEOPLASMHISTOLOGICGRADE"                         
[24] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[25] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[26] "TOBACCO_SMOKING_HISTORY"                         
[27] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[28] "RADIATION_TREATMENT_ADJUVANT"                    
[29] "RADIATION_THERAPY_TYPE"                          
[30] "RADIATION_THERAPY_STATUS"                        
[31] "RADIATION_ADJUVANT_UNITS"                        
[32] "PREGNANCIES_COUNT_TOTAL"                         
[33] "PREGNANCIES_COUNT_STILLBIRTH"                    
[34] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[35] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[36] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[37] "PREGNANCIES_COUNT_ECTOPIC"                       
[38] "PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT"    
[39] "LYMPH_NODE_LOCATION"                             
[40] "LOCATION_OF_POSITIVE_MARGINS"                    
[41] "MENOPAUSE_STATUS"                                
[42] "LYMPHOVASCULAR_INVOLVEMENT"                      
[43] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[44] "LYMPH_NODES_EXAMINED"                            
[45] "KERATINIZATION_SQUAMOUS_CELL"                    
[46] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[47] "HYSTERECTOMY_TYPE"                               
[48] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[49] "HEIGHT_CM_AT_DIAGNOSIS"                          
[50] "FEDPET_OR_CT_RESULTS"                            
[51] "CORPUS_INVOLVEMENT"                              
[52] "CHEMO_CONCURRENT_TYPE"                           
[53] "CERVIX_SUV_RESULTS"                              
[54] "CAUSE_OF_DEATH"                                  
[55] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[56] "AGE_AT_DIAGNOSIS"                                

Input Data has 56 rows and 176 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
        1505         1735          720           NA           NA           NA 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN 
        1112         4385         5385         5271           NA           NA 
TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
          NA           NA           NA         1409          919           NA 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK 
        1756         1617           NA           NA           NA           NA 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
          NA          109         1345         2226         2234         2526 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
        2383           NA         1169           25         1582          548 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
          NA          621         5564          771           NA           NA 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
          NA          294         2233           NA         2602         1846 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
          NA           NA           NA           83         2669         1791 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
          NA           81         3589         3609          699          512 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
          NA          223           NA           23          376           53 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
          40           25           19          397           36          441 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
          41           41          441           55          385          390 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
           8          453           45          423           21          456 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
         455          413          410          383         1398          202 
TCGA-EK-A2PG TCGA-EK-A2PI TCGA-EK-A2PK TCGA-EK-A2PL TCGA-EK-A2PM TCGA-EK-A2R7 
          16           NA           NA           NA           NA           18 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RK 
           2          123            1           11           36           NA 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
         721           68            3            2            3            3 
TCGA-EK-A3GM TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
          NA            1          619          241          211          447 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
         136          186           37          725           28           66 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
          20           31           44           48           45           25 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
         107           41           40           60           34          773 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
          NA          632          454          125         4483         4172 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
          NA         3571         2949         2394         2493          808 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
        1106          439          506          588          623          474 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AV TCGA-LP-A4AW TCGA-LP-A4AX 
         306          156            3           NA           27            2 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
          25          422            1          165          904            2 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
         132           90          113          105          178          103 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
         113          175          146          190          596          118 
TCGA-UC-A7PD TCGA-UC-A7PF 
          NA           NA 
Variable 1:'AGE':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=122,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=13,	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:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'HISTOLOGICAL.TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBERPACKYEARSSMOKED':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH.NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'WEIGHT_KG_AT_DIAGNOSIS':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'TUMOR_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'TUMOR_SAMPLE_PROCUREMENT_COUNTRY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'NEOPLASMHISTOLOGICGRADE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'TOBACCO_SMOKING_YEAR_STOPPED':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 25:'TOBACCO_SMOKING_PACK_YEARS_SMOKED':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'TOBACCO_SMOKING_HISTORY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 27:'PATIENT.AGEBEGANSMOKINGINYEARS':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 28:'RADIATION_TREATMENT_ADJUVANT':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'RADIATION_THERAPY_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 30:'RADIATION_THERAPY_STATUS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 31:'RADIATION_ADJUVANT_UNITS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 32:'PREGNANCIES_COUNT_TOTAL':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 33:'PREGNANCIES_COUNT_STILLBIRTH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 34:'PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 35:'PREGNANCIES_COUNT_LIVE_BIRTH':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 36:'PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 37:'PREGNANCIES_COUNT_ECTOPIC':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 38:'PATIENT.CERVICALCARCINOMAPELVICEXTENSIONTEXT':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 39:'LYMPH_NODE_LOCATION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 40:'LOCATION_OF_POSITIVE_MARGINS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 41:'MENOPAUSE_STATUS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 42:'LYMPHOVASCULAR_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 43:'LYMPH_NODES_EXAMINED_HE_COUNT':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 44:'LYMPH_NODES_EXAMINED':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 45:'KERATINIZATION_SQUAMOUS_CELL':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 46:'INITIAL_PATHOLOGIC_DX_YEAR':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 47:'HYSTERECTOMY_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 48:'HISTORY_HORMONAL_CONTRACEPTIVES_USE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 49:'HEIGHT_CM_AT_DIAGNOSIS':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 50:'FEDPET_OR_CT_RESULTS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 51:'CORPUS_INVOLVEMENT':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 52:'CHEMO_CONCURRENT_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 53:'CERVIX_SUV_RESULTS':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 54:'CAUSE_OF_DEATH':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 55:'AJCC_TUMOR_PATHOLOGIC_PT':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 56:'AGE_AT_DIAGNOSIS':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                             
 [2] "PATHOLOGY.T.STAGE"                               
 [3] "PATHOLOGY.N.STAGE"                               
 [4] "PATHOLOGY.M.STAGE"                               
 [5] "HISTOLOGICAL.TYPE"                               
 [6] "RADIATIONS.RADIATION.REGIMENINDICATION"          
 [7] "NUMBERPACKYEARSSMOKED"                           
 [8] "NUMBER.OF.LYMPH.NODES"                           
 [9] "RACE"                                            
[10] "ETHNICITY"                                       
[11] "WEIGHT_KG_AT_DIAGNOSIS"                          
[12] "TUMOR_STATUS"                                    
[13] "TUMOR_SAMPLE_PROCUREMENT_COUNTRY"                
[14] "NEOPLASMHISTOLOGICGRADE"                         
[15] "TOBACCO_SMOKING_YEAR_STOPPED"                    
[16] "TOBACCO_SMOKING_PACK_YEARS_SMOKED"               
[17] "TOBACCO_SMOKING_HISTORY"                         
[18] "PATIENT.AGEBEGANSMOKINGINYEARS"                  
[19] "RADIATION_THERAPY_TYPE"                          
[20] "RADIATION_ADJUVANT_UNITS"                        
[21] "PREGNANCIES_COUNT_TOTAL"                         
[22] "PREGNANCIES_COUNT_STILLBIRTH"                    
[23] "PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT"
[24] "PREGNANCIES_COUNT_LIVE_BIRTH"                    
[25] "PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT"
[26] "PREGNANCIES_COUNT_ECTOPIC"                       
[27] "LOCATION_OF_POSITIVE_MARGINS"                    
[28] "MENOPAUSE_STATUS"                                
[29] "LYMPHOVASCULAR_INVOLVEMENT"                      
[30] "LYMPH_NODES_EXAMINED_HE_COUNT"                   
[31] "LYMPH_NODES_EXAMINED"                            
[32] "KERATINIZATION_SQUAMOUS_CELL"                    
[33] "INITIAL_PATHOLOGIC_DX_YEAR"                      
[34] "HYSTERECTOMY_TYPE"                               
[35] "HISTORY_HORMONAL_CONTRACEPTIVES_USE"             
[36] "HEIGHT_CM_AT_DIAGNOSIS"                          
[37] "CORPUS_INVOLVEMENT"                              
[38] "CERVIX_SUV_RESULTS"                              
[39] "AJCC_TUMOR_PATHOLOGIC_PT"                        
[40] "AGE_AT_DIAGNOSIS"                                
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 176 columns, 1 survival variables, and 40 non-survival variables.
AGE, nv=54, binary=FALSE, numeric=TRUE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
97 36  2  1 
[1] "table(vv)"
vv
      T1 T2+T3+T4 
      97       39 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
97 36  2  1 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 97

$Class1_nSamples
[1] 39

$Class0_label
[1] "T1"

$Class1_label
[1] "T2+T3+T4"


      T1 T2+T3+T4 
      97       39 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=6, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=24, 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=63, binary=FALSE, numeric=TRUE
TUMOR_STATUS, nv=2, binary=FALSE, numeric=FALSE
TUMOR_SAMPLE_PROCUREMENT_COUNTRY, nv=5, binary=FALSE, numeric=FALSE
NEOPLASMHISTOLOGICGRADE, nv=5, binary=FALSE, numeric=FALSE
TOBACCO_SMOKING_YEAR_STOPPED, nv=16, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_PACK_YEARS_SMOKED, nv=24, binary=FALSE, numeric=TRUE
TOBACCO_SMOKING_HISTORY, nv=5, binary=FALSE, numeric=FALSE
PATIENT.AGEBEGANSMOKINGINYEARS, nv=20, binary=FALSE, numeric=TRUE
RADIATION_THERAPY_TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATION_ADJUVANT_UNITS, nv=2, binary=FALSE, numeric=FALSE
PREGNANCIES_COUNT_TOTAL, nv=13, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_STILLBIRTH, nv=3, binary=FALSE, numeric=TRUE
PATIENT.PATIENTPREGNANCYSPONTANEOUSABORTIONCOUNT, nv=4, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_LIVE_BIRTH, nv=10, binary=FALSE, numeric=TRUE
PATIENT.PATIENTPREGNANCYTHERAPEUTICABORTIONCOUNT, nv=7, binary=FALSE, numeric=TRUE
PREGNANCIES_COUNT_ECTOPIC, nv=3, binary=FALSE, numeric=TRUE
LOCATION_OF_POSITIVE_MARGINS, 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=46, binary=FALSE, numeric=TRUE
KERATINIZATION_SQUAMOUS_CELL, nv=2, binary=FALSE, numeric=FALSE
INITIAL_PATHOLOGIC_DX_YEAR, nv=19, binary=FALSE, numeric=TRUE
HYSTERECTOMY_TYPE, nv=3, binary=FALSE, numeric=FALSE
HISTORY_HORMONAL_CONTRACEPTIVES_USE, nv=3, binary=FALSE, numeric=FALSE
HEIGHT_CM_AT_DIAGNOSIS, nv=30, binary=FALSE, numeric=TRUE
CORPUS_INVOLVEMENT, nv=2, binary=FALSE, numeric=FALSE
CERVIX_SUV_RESULTS, nv=9, binary=FALSE, numeric=TRUE
AJCC_TUMOR_PATHOLOGIC_PT, nv=13, binary=FALSE, numeric=FALSE
AGE_AT_DIAGNOSIS, nv=55, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED   43  8
  1P GAIN WILD-TYPE 94 24
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               51               118 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                24 
$`1P GAIN MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1M6 
       49.48        36.56       144.16       177.04        82.85        31.40 
TCGA-C5-A1M7 TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A2LZ TCGA-C5-A3HF 
       46.32        38.99         0.46         2.43       100.14        17.85 
TCGA-C5-A7CJ TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-EA-A1QS TCGA-EA-A3HQ 
      101.82         2.73        87.75         2.66         0.76         1.74 
TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD 
        0.62         1.35        14.50         1.81        13.91         0.69 
TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM 
       14.96        12.59         0.53         0.59         1.18         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A3EO 
        0.10         0.07         0.03         6.94         4.47         2.17 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A40J TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LC 
        1.45         1.58         1.35        20.78        14.93       117.40 
TCGA-IR-A3LL TCGA-JW-A5VK TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MY-A5BE TCGA-PN-A8MA 
       36.36        20.48         0.82        13.87         0.07         2.96 
TCGA-Q1-A5R2 TCGA-R2-A69V TCGA-UC-A7PF 
        3.45        19.59        93.99 

$`1P GAIN WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BL 
       57.04        23.67        11.44        68.84        18.74       173.29 
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-A1MI TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       53.16        35.61        40.93         3.58        44.22        73.18 
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         0.82        52.01 
TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL 
       18.02        20.42       182.93        25.35       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
        9.67        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
        9.34        13.61        58.88        36.76       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT 
       22.98        16.83        16.18         7.33         8.28        12.36 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        1.32         0.82        13.05         1.18        14.50         1.35 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZE 
       12.66        12.82         0.26        14.89         1.48        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC 
       13.58        13.48        45.96         6.64         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 
        0.03         0.36        23.70         0.10         0.10        20.35 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        7.92        14.70         6.12         1.22        23.84         0.92 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        0.66         1.02         1.48         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.97         1.12        25.41        21.67         4.11       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        26.56 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       14.43        16.64        19.33        15.58        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.10         0.89         0.07         0.03         5.42        29.72 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34         3.72         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD 
        4.80         6.25         3.88        11.67 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           177.04            182.93 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            4.470            14.465 
[1] "0.0 - 177.0 (4.5)"  "0.0 - 182.9 (14.5)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                T1 T2+T3+T4
  1P GAIN MUTATED   26       14
  1P GAIN WILD-TYPE 71       25
D1V3, multiclass
          clus
vv         1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1                    26                71
  T2+T3+T4              14                25
[1] 2 2
[1] FALSE
D1V4, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   25 13
  1P GAIN WILD-TYPE 62 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     25   13
  1P GAIN WILD-TYPE   62   27
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              25                62
  1              13                27
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1P GAIN MUTATED   24  0 17
  1P GAIN WILD-TYPE 48  3 48
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              24                48
  M1               0                 3
  MX              17                48
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED               0                               49
  1P GAIN WILD-TYPE             2                               95
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1P GAIN MUTATED                                               0
  1P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1P GAIN MUTATED                                     3
  1P GAIN WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1P GAIN MUTATED                                           0
  1P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1P GAIN MUTATED                                              2
  1P GAIN WILD-TYPE                                            2
D1V6, multiclass
                                               clus
vv                                              1P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           49
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              1P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                             95
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  2
[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"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     8  46
  1P GAIN WILD-TYPE  19 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8   46
  1P GAIN WILD-TYPE   19  103
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                8                19
  YES              46               103
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  1     7
  1P GAIN WILD-TYPE                                6     8
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED                           7
  1P GAIN WILD-TYPE                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           0    38
  1P GAIN WILD-TYPE                                         1    92
D1V10, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   7                 8
  BLACK OR AFRICAN AMERICAN                               7                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  38                92
[1] 5 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    1 41
  1P GAIN WILD-TYPE 10 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   41
  1P GAIN WILD-TYPE   10   86
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              41                86
[1] 2 2
[1] FALSE
D1V12, continuous
D1V13, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   12  6
  1P GAIN WILD-TYPE 36 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     12    6
  1P GAIN WILD-TYPE   36   13
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  TUMOR FREE              12                36
  WITH TUMOR               6                13
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  1P GAIN MUTATED         1      4       2            42       5
  1P GAIN WILD-TYPE       0      6       4           105       7
D1V14, multiclass
               clus
vv              1P GAIN MUTATED 1P GAIN WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      4                 6
  UKRAINE                     2                 4
  UNITED STATES              42               105
  VIETNAM                     5                 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                G1 G2 G3 G4 GX
  1P GAIN MUTATED    2 27 25  0  0
  1P GAIN WILD-TYPE 12 56 47  1  5
D1V15, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  G1               2                12
  G2              27                56
  G3              25                47
  G4               0                 1
  GX               0                 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"
D1V16, continuous
D1V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  1P GAIN MUTATED                                             4
  1P GAIN WILD-TYPE                                          17
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  1P GAIN MUTATED                                        3
  1P GAIN WILD-TYPE                                      5
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  1P GAIN MUTATED                                                 0
  1P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1P GAIN MUTATED               10                  26
  1P GAIN WILD-TYPE             26                  57
D1V18, multiclass
                                                 clus
vv                                                1P 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                                          26
                                                 clus
vv                                                1P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 26
  LIFELONG NON-SMOKER                                            57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  1P GAIN MUTATED             7       10             1        0
  1P GAIN WILD-TYPE          10       27            10        5
D1V20, multiclass
               clus
vv              1P GAIN MUTATED 1P GAIN WILD-TYPE
  COMBINATION                 7                10
  EXTERNAL                   10                27
  EXTERNAL BEAM               1                10
  INTERNAL                    0                 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"
D1V21, binary
                   cls
clus                0 1
  1P GAIN MUTATED   2 1
  1P GAIN WILD-TYPE 9 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    1
  1P GAIN WILD-TYPE    9    2
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  CGY               2                 9
  GY                1                 2
[1] 2 2
[1] FALSE
D1V22, continuous
D1V23, continuous
D1V24, continuous
D1V25, continuous
D1V26, continuous
D1V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  1P GAIN MUTATED                                     1
  1P GAIN WILD-TYPE                                   1
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  1P GAIN MUTATED                                     0                       3
  1P GAIN WILD-TYPE                                   6                       6
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1P GAIN MUTATED                         0                       2
  1P GAIN WILD-TYPE                       1                       3
D1V28, multiclass
                                     clus
vv                                    1P GAIN MUTATED 1P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           3                 6
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 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)
  1P GAIN MUTATED                                               0
  1P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  1P GAIN MUTATED                                                2
  1P GAIN WILD-TYPE                                              8
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1P GAIN MUTATED                                                                                  23
  1P GAIN WILD-TYPE                                                                                31
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1P GAIN MUTATED                                                                                             22
  1P GAIN WILD-TYPE                                                                                           55
D1V29, multiclass
                                                                                              clus
vv                                                                                             1P 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)                         23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              22
                                                                                              clus
vv                                                                                             1P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               8
  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)                55
[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"
D1V30, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   16 18
  1P GAIN WILD-TYPE 38 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     16   18
  1P GAIN WILD-TYPE   38   41
         clus
vv        1P GAIN MUTATED 1P GAIN WILD-TYPE
  ABSENT               16                38
  PRESENT              18                41
[1] 2 2
[1] FALSE
D1V31, continuous
D1V32, continuous
D1V33, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   11 24
  1P GAIN WILD-TYPE 24 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     11   24
  1P GAIN WILD-TYPE   24   57
                                          clus
vv                                         1P GAIN MUTATED 1P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  11                24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              24                57
[1] 2 2
[1] FALSE
D1V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  1P GAIN MUTATED       0                   36                   0
  1P GAIN WILD-TYPE     3                   77                   5
D1V35, multiclass
                      clus
vv                     1P GAIN MUTATED 1P GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              36                77
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1P GAIN MUTATED              3           8         12
  1P GAIN WILD-TYPE            5          32         28
D1V36, multiclass
              clus
vv             1P GAIN MUTATED 1P GAIN WILD-TYPE
  CURRENT USER               3                 5
  FORMER USER                8                32
  NEVER USED                12                28
[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, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   21  5
  1P GAIN WILD-TYPE 52  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     21    5
  1P GAIN WILD-TYPE   52    9
         clus
vv        1P GAIN MUTATED 1P GAIN WILD-TYPE
  ABSENT               21                52
  PRESENT               5                 9
[1] 2 2
[1] FALSE
D1V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  1P GAIN MUTATED     1    0   6   15    4  1   3    4    0   6   0  0  2
  1P GAIN WILD-TYPE   1    1  16   36   17  2   3    2    8   7   2  1  5
D1V40, multiclass
      clus
vv     1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1A                1                 1
  T1A1               0                 1
  T1B                6                16
  T1B1              15                36
  T1B2               4                17
  T2                 1                 2
  T2A                3                 3
  T2A1               4                 2
  T2A2               0                 8
  T2B                6                 7
  T3B                0                 2
  T4                 0                 1
  TX                 2                 5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V41, continuous

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   63 15
  1Q GAIN WILD-TYPE 74 17
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               78                91 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               15                17 
$`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-A1MP TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2LZ 
        0.46         2.43         3.58        44.22        78.35       100.14 
TCGA-C5-A3HF TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UI TCGA-C5-A7X8 
       17.85       101.82       134.33        15.48        94.95         2.73 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-DS-A7WI 
       87.75        58.88         2.66        22.98         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A411 TCGA-EA-A439 
        0.76         1.74         1.32         0.62         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.81        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RJ 
       13.48        12.59        45.96         0.53         0.59         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A449 
        2.24         0.10         0.10         0.03         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A40J 
        4.47         6.12        23.84         2.17         1.45         1.35 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LC TCGA-IR-A3LL TCGA-JW-A5VJ 
       20.78        14.93         4.11       117.40        36.36        19.33 
TCGA-JW-A5VK TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MY-A5BE 
       20.48         5.13         0.10         0.82        13.87         0.07 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PF 
        2.96         3.45         5.85         6.25        19.59        93.99 

$`1Q GAIN WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BQ TCGA-C5-A1M5 
       57.04        23.67        11.44        68.84        19.86        67.46 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LT 
       30.21        35.01        57.73        35.61        40.93        73.18 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       73.45        83.05        38.43         0.82        52.01        18.02 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
       20.42       182.93        25.35         9.67        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DS-A0VK TCGA-DS-A0VM 
       85.55        60.69         9.34        13.61        36.76       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A3HS TCGA-EA-A3QD 
      118.65        16.83        16.18        12.36         0.82        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.18        14.50         1.35        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       14.89         1.48         6.64         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.36        23.70         0.07         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         0.92         0.66         1.02         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         3.52         1.32         1.97         1.12        25.41 
TCGA-HM-A3JJ TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH 
       21.67       147.39       137.16        66.81        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VL TCGA-JW-A69B 
       81.96        26.56        14.43        16.64        15.58        10.06 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF 
        0.89         0.07         0.03         5.42        29.72         4.34 
TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-RA-A741 
        3.72         3.39         3.72         5.75         4.80         3.88 
TCGA-UC-A7PD 
       11.67 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           177.04            182.93 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            13.53             13.61 
[1] "0.0 - 177.0 (13.5)" "0.0 - 182.9 (13.6)"
[1] "hr=" "1"  
D2V2, continuous
                   vv
clus                T1 T2+T3+T4
  1Q GAIN MUTATED   39       22
  1Q GAIN WILD-TYPE 58       17
D2V3, multiclass
          clus
vv         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                    39                58
  T2+T3+T4              22                17
[1] 2 2
[1] FALSE
D2V4, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   37 20
  1Q GAIN WILD-TYPE 50 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     37   20
  1Q GAIN WILD-TYPE   50   20
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              37                50
  1              20                20
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED   35  2 28
  1Q GAIN WILD-TYPE 37  1 37
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              35                37
  M1               2                 1
  MX              28                37
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED               1                               71
  1Q GAIN WILD-TYPE             1                               73
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1Q GAIN MUTATED                                               1
  1Q GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1Q GAIN MUTATED                                     8
  1Q GAIN WILD-TYPE                                  12
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1Q GAIN MUTATED                                           0
  1Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1Q GAIN MUTATED                                              2
  1Q GAIN WILD-TYPE                                            2
D2V6, multiclass
                                               clus
vv                                              1Q GAIN MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           71
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              1Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 1
  CERVICAL SQUAMOUS CELL CARCINOMA                             73
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  2
[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"
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   15 68
  1Q GAIN WILD-TYPE 12 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     15   68
  1Q GAIN WILD-TYPE   12   81
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               15                12
  YES              68                81
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1    11
  1Q GAIN WILD-TYPE                                6     4
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED                          10
  1Q GAIN WILD-TYPE                         8
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           0    59
  1Q GAIN WILD-TYPE                                         1    71
D2V10, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                  11                 4
  BLACK OR AFRICAN AMERICAN                              10                 8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  59                71
[1] 5 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    3 59
  1Q GAIN WILD-TYPE  8 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3   59
  1Q GAIN WILD-TYPE    8   68
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              59                68
[1] 2 2
[1] FALSE
D2V12, continuous
D2V13, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   22 10
  1Q GAIN WILD-TYPE 26  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     22   10
  1Q GAIN WILD-TYPE   26    9
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  TUMOR FREE              22                26
  WITH TUMOR              10                 9
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  1Q GAIN MUTATED         1      5       2            66       9
  1Q GAIN WILD-TYPE       0      5       4            81       3
D2V14, multiclass
               clus
vv              1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      5                 5
  UKRAINE                     2                 4
  UNITED STATES              66                81
  VIETNAM                     9                 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                G1 G2 G3 G4 GX
  1Q GAIN MUTATED    4 40 38  0  1
  1Q GAIN WILD-TYPE 10 43 34  1  4
D2V15, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  G1               4                10
  G2              40                43
  G3              38                34
  G4               0                 1
  GX               1                 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"
D2V16, continuous
D2V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  1Q GAIN MUTATED                                             7
  1Q GAIN WILD-TYPE                                          14
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  1Q GAIN MUTATED                                        4
  1Q GAIN WILD-TYPE                                      4
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  1Q GAIN MUTATED                                                 1
  1Q GAIN WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1Q GAIN MUTATED               16                  41
  1Q GAIN WILD-TYPE             20                  42
D2V18, multiclass
                                                 clus
vv                                                1Q 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                                               16
  LIFELONG NON-SMOKER                                          41
                                                 clus
vv                                                1Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 20
  LIFELONG NON-SMOKER                                            42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  1Q GAIN MUTATED            12       17             3        1
  1Q GAIN WILD-TYPE           5       20             8        4
D2V20, multiclass
               clus
vv              1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COMBINATION                12                 5
  EXTERNAL                   17                20
  EXTERNAL BEAM               3                 8
  INTERNAL                    1                 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"
D2V21, binary
                   cls
clus                0 1
  1Q GAIN MUTATED   3 2
  1Q GAIN WILD-TYPE 8 1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3    2
  1Q GAIN WILD-TYPE    8    1
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CGY               3                 8
  GY                2                 1
[1] 2 2
[1] FALSE
D2V22, continuous
D2V23, continuous
D2V24, continuous
D2V25, continuous
D2V26, continuous
D2V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  1Q GAIN MUTATED                                     1
  1Q GAIN WILD-TYPE                                   1
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  1Q GAIN MUTATED                                     0                       5
  1Q GAIN WILD-TYPE                                   6                       4
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1Q GAIN MUTATED                         0                       2
  1Q GAIN WILD-TYPE                       1                       3
D2V28, multiclass
                                     clus
vv                                    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           5                 4
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 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)
  1Q GAIN MUTATED                                               0
  1Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  1Q GAIN MUTATED                                                5
  1Q GAIN WILD-TYPE                                              5
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1Q GAIN MUTATED                                                                                  28
  1Q GAIN WILD-TYPE                                                                                26
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1Q GAIN MUTATED                                                                                             36
  1Q GAIN WILD-TYPE                                                                                           41
D2V29, multiclass
                                                                                              clus
vv                                                                                             1Q 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)                         28
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              36
                                                                                              clus
vv                                                                                             1Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               5
  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)                41
[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"
D2V30, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   23 27
  1Q GAIN WILD-TYPE 31 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     23   27
  1Q GAIN WILD-TYPE   31   32
         clus
vv        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ABSENT               23                31
  PRESENT              27                32
[1] 2 2
[1] FALSE
D2V31, continuous
D2V32, continuous
D2V33, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   14 39
  1Q GAIN WILD-TYPE 21 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     14   39
  1Q GAIN WILD-TYPE   21   42
                                          clus
vv                                         1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  14                21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              39                42
[1] 2 2
[1] FALSE
D2V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  1Q GAIN MUTATED       1                   50                   1
  1Q GAIN WILD-TYPE     2                   63                   4
D2V35, multiclass
                      clus
vv                     1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  OTHER                              1                 2
  RADICAL HYSTERECTOMY              50                63
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1Q GAIN MUTATED              4          16         18
  1Q GAIN WILD-TYPE            4          24         22
D2V36, multiclass
              clus
vv             1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CURRENT USER               4                 4
  FORMER USER               16                24
  NEVER USED                18                22
[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, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   31  6
  1Q GAIN WILD-TYPE 42  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     31    6
  1Q GAIN WILD-TYPE   42    8
         clus
vv        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ABSENT               31                42
  PRESENT               6                 8
[1] 2 2
[1] FALSE
D2V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  1Q GAIN MUTATED     1    0   7   23    8  2   5    5    1   8   1  0  5
  1Q GAIN WILD-TYPE   1    1  15   28   13  1   1    1    7   5   1  1  2
D2V40, multiclass
      clus
vv     1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1A                1                 1
  T1A1               0                 1
  T1B                7                15
  T1B1              23                28
  T1B2               8                13
  T2                 2                 1
  T2A                5                 1
  T2A1               5                 1
  T2A2               1                 7
  T2B                8                 5
  T3B                1                 1
  T4                 0                 1
  TX                 5                 2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V41, continuous

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    26   7
  2P GAIN WILD-TYPE 111  25
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               33               136 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7                25 
$`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         0.82        60.69         9.34        13.61         2.73 
TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A556 
       22.98         7.33         1.35        14.50         1.81        14.89 
TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-EX-A1H6 
       14.96        12.59         1.18         2.24         0.10         7.92 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A40J TCGA-IR-A3LC TCGA-JW-A5VJ TCGA-Q1-A5R2 
       23.84         1.45         1.35       117.40        19.33         3.45 
TCGA-Q1-A5R3 TCGA-UC-A7PD TCGA-UC-A7PF 
        5.85        11.67        93.99 

$`2P 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-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK 
       46.32        30.21        35.01        53.16        38.99         2.43 
TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       40.93         3.58        44.22        73.45        83.05        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14        38.43        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 
      182.93        25.35       101.82       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-DR-A0ZL TCGA-DR-A0ZM 
       73.41        17.19        85.55        94.95        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       117.99       118.65        16.83        16.18 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S 
        0.62        13.05         1.18        14.50         1.35        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26         1.48        13.91         0.69        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.58        13.48        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN 
        0.07         4.04         0.03         0.36        23.70         0.10 
TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 
        0.07         0.10         0.03        20.35         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        4.47         6.12         1.22         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        1.02         1.58         1.48         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH 
        4.11       147.39       137.16        66.81        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK 
       81.96        26.56        36.36        14.43        16.64        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       15.58        10.06         5.13         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34         2.96         3.72         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        4.80         6.25        19.59         3.88 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           117.40            182.93 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            11.67             13.89 
[1] "0.1 - 117.4 (11.7)" "0.0 - 182.9 (13.9)"
[1] "hr=" "1.7"
D3V2, continuous
                   vv
clus                T1 T2+T3+T4
  2P GAIN MUTATED   17        6
  2P GAIN WILD-TYPE 80       33
D3V3, multiclass
          clus
vv         2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1                    17                80
  T2+T3+T4               6                33
[1] 2 2
[1] FALSE
D3V4, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   15  6
  2P GAIN WILD-TYPE 72 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15    6
  2P GAIN WILD-TYPE   72   34
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              15                72
  1               6                34
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2P GAIN MUTATED   14  0 10
  2P GAIN WILD-TYPE 58  3 55
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              14                58
  M1               0                 3
  MX              10                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED               0                               27
  2P GAIN WILD-TYPE             2                              117
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2P GAIN MUTATED                                               0
  2P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2P GAIN MUTATED                                     6
  2P GAIN WILD-TYPE                                  14
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2P GAIN MUTATED                                           1
  2P GAIN WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2P GAIN MUTATED                                              1
  2P GAIN WILD-TYPE                                            3
D3V6, multiclass
                                               clus
vv                                              2P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           27
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         6
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              2P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            117
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          14
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     5  30
  2P GAIN WILD-TYPE  22 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5   30
  2P GAIN WILD-TYPE   22  119
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                5                22
  YES              30               119
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  2     2
  2P GAIN WILD-TYPE                                5    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED                           2
  2P GAIN WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           1    26
  2P GAIN WILD-TYPE                                         0   104
D3V10, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 5
  ASIAN                                                   2                13
  BLACK OR AFRICAN AMERICAN                               2                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  26               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"
D3V11, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1  23
  2P GAIN WILD-TYPE  10 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1   23
  2P GAIN WILD-TYPE   10  104
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              23               104
[1] 2 2
[1] FALSE
D3V12, continuous
D3V13, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    8  5
  2P GAIN WILD-TYPE 40 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8    5
  2P GAIN WILD-TYPE   40   14
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  TUMOR FREE               8                40
  WITH TUMOR               5                14
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  2P GAIN MUTATED         0      2       1            30       2
  2P GAIN WILD-TYPE       1      8       5           117      10
D3V14, multiclass
               clus
vv              2P GAIN MUTATED 2P GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      2                 8
  UKRAINE                     1                 5
  UNITED STATES              30               117
  VIETNAM                     2                10
[1] 5 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                G1 G2 G3 G4 GX
  2P GAIN MUTATED    2 15 18  0  0
  2P GAIN WILD-TYPE 12 68 54  1  5
D3V15, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  G1               2                12
  G2              15                68
  G3              18                54
  G4               0                 1
  GX               0                 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"
D3V16, continuous
D3V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2P GAIN MUTATED                                             2
  2P GAIN WILD-TYPE                                          19
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  2P GAIN MUTATED                                        1
  2P GAIN WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  2P GAIN MUTATED                                                 0
  2P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2P GAIN MUTATED                8                  16
  2P GAIN WILD-TYPE             28                  67
D3V18, multiclass
                                                 clus
vv                                                2P 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                                                8
  LIFELONG NON-SMOKER                                          16
                                                 clus
vv                                                2P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 28
  LIFELONG NON-SMOKER                                            67
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  2P GAIN MUTATED             3        8             2        2
  2P GAIN WILD-TYPE          14       29             9        3
D3V20, multiclass
               clus
vv              2P GAIN MUTATED 2P GAIN WILD-TYPE
  COMBINATION                 3                14
  EXTERNAL                    8                29
  EXTERNAL BEAM               2                 9
  INTERNAL                    2                 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"
D3V21, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    1  0
  2P GAIN WILD-TYPE 10  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1    0
  2P GAIN WILD-TYPE   10    3
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  CGY               1                10
  GY                0                 3
[1] 2 2
[1] FALSE
D3V22, continuous
D3V23, continuous
D3V24, continuous
D3V25, continuous
D3V26, continuous
D3V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  2P GAIN MUTATED                                     0
  2P GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  2P GAIN MUTATED                                     1                       2
  2P GAIN WILD-TYPE                                   5                       7
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2P GAIN MUTATED                         0                       0
  2P GAIN WILD-TYPE                       1                       5
D3V28, multiclass
                                     clus
vv                                    2P GAIN MUTATED 2P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           2                 7
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 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)
  2P GAIN MUTATED                                               0
  2P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  2P GAIN MUTATED                                                2
  2P GAIN WILD-TYPE                                              8
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2P GAIN MUTATED                                                                                  10
  2P GAIN WILD-TYPE                                                                                44
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2P GAIN MUTATED                                                                                             14
  2P GAIN WILD-TYPE                                                                                           63
D3V29, multiclass
                                                                                              clus
vv                                                                                             2P 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)                         10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              14
                                                                                              clus
vv                                                                                             2P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               8
  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)                63
[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"
D3V30, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    7 14
  2P GAIN WILD-TYPE 47 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      7   14
  2P GAIN WILD-TYPE   47   45
         clus
vv        2P GAIN MUTATED 2P GAIN WILD-TYPE
  ABSENT                7                47
  PRESENT              14                45
[1] 2 2
[1] FALSE
D3V31, continuous
D3V32, continuous
D3V33, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    7 12
  2P GAIN WILD-TYPE 28 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      7   12
  2P GAIN WILD-TYPE   28   69
                                          clus
vv                                         2P GAIN MUTATED 2P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   7                28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              12                69
[1] 2 2
[1] FALSE
D3V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  2P GAIN MUTATED       0                   22                   0
  2P GAIN WILD-TYPE     3                   91                   5
D3V35, multiclass
                      clus
vv                     2P GAIN MUTATED 2P GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              22                91
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2P GAIN MUTATED              3          11          5
  2P GAIN WILD-TYPE            5          29         35
D3V36, multiclass
              clus
vv             2P GAIN MUTATED 2P GAIN WILD-TYPE
  CURRENT USER               3                 5
  FORMER USER               11                29
  NEVER USED                 5                35
[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
D3V38, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   11  4
  2P GAIN WILD-TYPE 62 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     11    4
  2P GAIN WILD-TYPE   62   10
         clus
vv        2P GAIN MUTATED 2P GAIN WILD-TYPE
  ABSENT               11                62
  PRESENT               4                10
[1] 2 2
[1] FALSE
D3V39, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                 8 
       TCGA-C5-A1MH        TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-EK-A2RO 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  2P GAIN MUTATED     0    0   2   14    1  0   1    3    0   1   1  0  2
  2P GAIN WILD-TYPE   2    1  20   37   20  3   5    3    8  12   1  1  5
D3V40, multiclass
      clus
vv     2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                2                20
  T1B1              14                37
  T1B2               1                20
  T2                 0                 3
  T2A                1                 5
  T2A1               3                 3
  T2A2               0                 8
  T2B                1                12
  T3B                1                 1
  T4                 0                 1
  TX                 2                 5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V41, continuous

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    16   6
  2Q GAIN WILD-TYPE 121  26
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               22               147 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                26 
$`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        60.69 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A411 TCGA-EA-A439 
        9.34         2.73         7.33         8.28         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-FU-A3NI 
        1.81        14.96        12.59         1.18         2.24         1.45 
TCGA-FU-A40J TCGA-Q1-A5R2 TCGA-UC-A7PD TCGA-UC-A7PF 
        1.35         3.45        11.67        93.99 

$`2Q 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-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-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
       38.99         2.43        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         0.82        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       182.93        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48         9.67        73.41        17.19        85.55 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       94.95        13.61        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A1QS 
      117.99       118.65        22.98        16.83        16.18         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       12.36         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.18        14.50         1.35        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       14.89         1.48        13.91         0.69        14.99        13.58 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB 
       13.48        45.96         6.64         0.53         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
        4.04         0.03         0.36        23.70         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         4.47         6.12         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17         0.66         1.02         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        3.52         1.32         1.97         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         4.11       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       14.43        16.64        19.33        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
        5.13         0.10         0.89         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.72         5.85         3.39         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        6.25        19.59         3.88 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.46              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            93.99            182.93 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             8.81             13.91 
[1] "0.5 - 94.0 (8.8)"   "0.0 - 182.9 (13.9)"
[1] "hr=" "2.6"
D4V2, continuous
                   vv
clus                T1 T2+T3+T4
  2Q GAIN MUTATED   12        4
  2Q GAIN WILD-TYPE 85       35
D4V3, multiclass
          clus
vv         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1                    12                85
  T2+T3+T4               4                35
[1] 2 2
[1] FALSE
D4V4, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    9  6
  2Q GAIN WILD-TYPE 78 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9    6
  2Q GAIN WILD-TYPE   78   34
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               9                78
  1               6                34
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2Q GAIN MUTATED   10  0  7
  2Q GAIN WILD-TYPE 62  3 58
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              10                62
  M1               0                 3
  MX               7                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED               0                               20
  2Q GAIN WILD-TYPE             2                              124
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2Q GAIN MUTATED                                               0
  2Q GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2Q GAIN MUTATED                                     3
  2Q GAIN WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2Q GAIN MUTATED                                           0
  2Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2Q GAIN MUTATED                                              1
  2Q GAIN WILD-TYPE                                            3
D4V6, multiclass
                                               clus
vv                                              2Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           20
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              2Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            124
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     3  21
  2Q GAIN WILD-TYPE  24 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   21
  2Q GAIN WILD-TYPE   24  128
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                3                24
  YES              21               128
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  1     2
  2Q GAIN WILD-TYPE                                6    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED                           1
  2Q GAIN WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           0    19
  2Q GAIN WILD-TYPE                                         1   111
D4V10, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   2                13
  BLACK OR AFRICAN AMERICAN                               1                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  19               111
[1] 5 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     0  18
  2Q GAIN WILD-TYPE  11 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   18
  2Q GAIN WILD-TYPE   11  109
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              18               109
[1] 2 2
[1] FALSE
D4V12, continuous
D4V13, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4  4
  2Q GAIN WILD-TYPE 44 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    4
  2Q GAIN WILD-TYPE   44   15
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  TUMOR FREE               4                44
  WITH TUMOR               4                15
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  2Q GAIN MUTATED         0      1       1            20       2
  2Q GAIN WILD-TYPE       1      9       5           127      10
D4V14, multiclass
               clus
vv              2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     1                 5
  UNITED STATES              20               127
  VIETNAM                     2                10
[1] 5 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                G1 G2 G3 G4 GX
  2Q GAIN MUTATED    0 14 10  0  0
  2Q GAIN WILD-TYPE 14 69 62  1  5
D4V15, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  G1               0                14
  G2              14                69
  G3              10                62
  G4               0                 1
  GX               0                 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"
D4V16, continuous
D4V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2Q GAIN MUTATED                                             0
  2Q GAIN WILD-TYPE                                          21
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  2Q GAIN MUTATED                                        0
  2Q GAIN WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  2Q GAIN MUTATED                                                 0
  2Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2Q GAIN MUTATED                6                  12
  2Q GAIN WILD-TYPE             30                  71
D4V18, multiclass
                                                 clus
vv                                                2Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                6
  LIFELONG NON-SMOKER                                          12
                                                 clus
vv                                                2Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 30
  LIFELONG NON-SMOKER                                            71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  2Q GAIN MUTATED             2        5             1        2
  2Q GAIN WILD-TYPE          15       32            10        3
D4V20, multiclass
               clus
vv              2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COMBINATION                 2                15
  EXTERNAL                    5                32
  EXTERNAL BEAM               1                10
  INTERNAL                    2                 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"
D4V21, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    0  0
  2Q GAIN WILD-TYPE 11  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0    0
  2Q GAIN WILD-TYPE   11    3
D4V22, continuous
D4V23, continuous
D4V24, continuous
D4V25, continuous
D4V26, continuous
D4V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  2Q GAIN MUTATED                                     0
  2Q GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  2Q GAIN MUTATED                                     1                       1
  2Q GAIN WILD-TYPE                                   5                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2Q GAIN MUTATED                         0                       0
  2Q GAIN WILD-TYPE                       1                       5
D4V28, multiclass
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                21 
       TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM        TCGA-C5-A2LX 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A50E        TCGA-EK-A2RN 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-MU-A8JM 
"2Q GAIN WILD-TYPE" 
                   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                                              8
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2Q GAIN MUTATED                                                                                   6
  2Q GAIN WILD-TYPE                                                                                48
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2Q GAIN MUTATED                                                                                              9
  2Q GAIN WILD-TYPE                                                                                           68
D4V29, 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)                          6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               9
                                                                                              clus
vv                                                                                             2Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               8
  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)                68
[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"
D4V30, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3 12
  2Q GAIN WILD-TYPE 51 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   12
  2Q GAIN WILD-TYPE   51   47
         clus
vv        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ABSENT                3                51
  PRESENT              12                47
[1] 2 2
[1] FALSE
D4V31, continuous
D4V32, continuous
D4V33, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    5 10
  2Q GAIN WILD-TYPE 30 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5   10
  2Q GAIN WILD-TYPE   30   71
                                          clus
vv                                         2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              10                71
[1] 2 2
[1] FALSE
D4V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  2Q GAIN MUTATED       0                   17                   0
  2Q GAIN WILD-TYPE     3                   96                   5
D4V35, multiclass
                      clus
vv                     2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              17                96
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2Q GAIN MUTATED              1           7          3
  2Q GAIN WILD-TYPE            7          33         37
D4V36, multiclass
              clus
vv             2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                7                33
  NEVER USED                 3                37
[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
D4V38, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    6  3
  2Q GAIN WILD-TYPE 67 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      6    3
  2Q GAIN WILD-TYPE   67   11
         clus
vv        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ABSENT                6                67
  PRESENT               3                11
[1] 2 2
[1] FALSE
D4V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  2Q GAIN MUTATED     0    0   2    9    1  0   1    2    1   0   0  0  1
  2Q GAIN WILD-TYPE   2    1  20   42   20  3   5    4    7  13   2  1  6
D4V40, multiclass
      clus
vv     2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                2                20
  T1B1               9                42
  T1B2               1                20
  T2                 0                 3
  T2A                1                 5
  T2A1               2                 4
  T2A2               1                 7
  T2B                0                13
  T3B                0                 2
  T4                 0                 1
  TX                 1                 6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V41, continuous

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    29  13
  3P GAIN WILD-TYPE 108  19
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               42               127 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13                19 
$`3P GAIN MUTATED`
TCGA-C5-A1BL TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF 
      173.29        31.40        46.32        30.21        35.01        53.16 
TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A2LT TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CJ 
       38.99         0.46        73.18        18.02        17.85       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7X3 TCGA-DS-A0VL TCGA-DS-A7WH TCGA-DS-A7WI 
      134.33        15.48         9.34         2.66         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A50E TCGA-EA-A5ZF TCGA-EK-A2GZ 
        0.76        13.05        14.50         0.26        14.96        12.59 
TCGA-EK-A2PG TCGA-EK-A2RC TCGA-EK-A2RM TCGA-EX-A69L TCGA-FU-A3NI TCGA-FU-A3TX 
        0.53         4.04         2.24         4.47         1.45         1.48 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LA TCGA-JW-A5VJ TCGA-JW-A852 
       25.41        21.67        20.78       137.16        19.33         5.13 
TCGA-LP-A4AU TCGA-MU-A8JM TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-UC-A7PD TCGA-UC-A7PF 
        0.10         5.42         2.96         3.72        11.67        93.99 

$`3P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       67.46        57.73        35.61         2.43        40.93         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-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM 
        0.82        52.01        20.42       182.93        25.35         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 
       73.41        17.19        85.55        60.69        94.95        13.61 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
        2.73        87.75        58.88        36.76       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       22.98        16.83        16.18        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.82         0.62         1.18        14.50         1.35         1.35 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        1.81        12.66        12.82        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP 
        0.69        14.99        13.58        13.48        45.96         6.64 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.59         0.07         0.03         0.36         1.18        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        7.92         6.94        14.70         6.12         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB 
        0.92         2.17         0.66         1.02         1.58         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A4S6 
        3.52         1.35         1.32         1.97         1.12        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
        4.11       147.39        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK 
       81.96        26.56        36.36        14.43        16.64        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
       15.58        10.06         0.89         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.03        29.72         0.07         4.34         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 
        3.88 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           173.29            182.93 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           13.775            13.580 
[1] "0.1 - 173.3 (13.8)" "0.0 - 182.9 (13.6)"
[1] "hr=" "2"  
D5V2, continuous
                   vv
clus                T1 T2+T3+T4
  3P GAIN MUTATED   22       10
  3P GAIN WILD-TYPE 75       29
D5V3, multiclass
          clus
vv         3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                    22                75
  T2+T3+T4              10                29
[1] 2 2
[1] FALSE
D5V4, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   18 12
  3P GAIN WILD-TYPE 69 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     18   12
  3P GAIN WILD-TYPE   69   28
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              18                69
  1              12                28
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3P GAIN MUTATED   18  0 14
  3P GAIN WILD-TYPE 54  3 51
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              18                54
  M1               0                 3
  MX              14                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED               0                               38
  3P GAIN WILD-TYPE             2                              106
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3P GAIN MUTATED                                               0
  3P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3P GAIN MUTATED                                     4
  3P GAIN WILD-TYPE                                  16
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3P GAIN MUTATED                                           1
  3P GAIN WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3P GAIN MUTATED                                              2
  3P GAIN WILD-TYPE                                            2
D5V6, multiclass
                                               clus
vv                                              3P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           38
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                2
                                               clus
vv                                              3P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            106
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  2
[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"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    10  35
  3P GAIN WILD-TYPE  17 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     10   35
  3P GAIN WILD-TYPE   17  114
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               10                17
  YES              35               114
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  2     5
  3P GAIN WILD-TYPE                                5    10
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED                           4
  3P GAIN WILD-TYPE                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           0    31
  3P GAIN WILD-TYPE                                         1    99
D5V10, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 5
  ASIAN                                                   5                10
  BLACK OR AFRICAN AMERICAN                               4                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  31                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"
D5V11, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    3 29
  3P GAIN WILD-TYPE  8 98
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   29
  3P GAIN WILD-TYPE    8   98
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              29                98
[1] 2 2
[1] FALSE
D5V12, continuous
D5V13, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   10  9
  3P GAIN WILD-TYPE 38 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     10    9
  3P GAIN WILD-TYPE   38   10
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  TUMOR FREE              10                38
  WITH TUMOR               9                10
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  3P GAIN MUTATED         1      1       0            39       4
  3P GAIN WILD-TYPE       0      9       6           108       8
D5V14, multiclass
               clus
vv              3P GAIN MUTATED 3P GAIN WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      1                 9
  UKRAINE                     0                 6
  UNITED STATES              39               108
  VIETNAM                     4                 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                G1 G2 G3 G4 GX
  3P GAIN MUTATED    0 26 19  0  0
  3P GAIN WILD-TYPE 14 57 53  1  5
D5V15, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  G1               0                14
  G2              26                57
  G3              19                53
  G4               0                 1
  GX               0                 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"
D5V16, continuous
D5V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3P GAIN MUTATED                                             5
  3P GAIN WILD-TYPE                                          16
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  3P GAIN MUTATED                                        1
  3P GAIN WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  3P GAIN MUTATED                                                 1
  3P GAIN WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3P GAIN MUTATED                9                  21
  3P GAIN WILD-TYPE             27                  62
D5V18, multiclass
                                                 clus
vv                                                3P 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                                          21
                                                 clus
vv                                                3P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 27
  LIFELONG NON-SMOKER                                            62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  3P GAIN MUTATED             5        8             5        2
  3P GAIN WILD-TYPE          12       29             6        3
D5V20, multiclass
               clus
vv              3P GAIN MUTATED 3P GAIN WILD-TYPE
  COMBINATION                 5                12
  EXTERNAL                    8                29
  EXTERNAL BEAM               5                 6
  INTERNAL                    2                 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"
D5V21, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  1
  3P GAIN WILD-TYPE 10  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    1
  3P GAIN WILD-TYPE   10    2
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  CGY               1                10
  GY                1                 2
[1] 2 2
[1] FALSE
D5V22, continuous
D5V23, continuous
D5V24, continuous
D5V25, continuous
D5V26, continuous
D5V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  3P GAIN MUTATED                                     0
  3P GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  3P GAIN MUTATED                                     1                       2
  3P GAIN WILD-TYPE                                   5                       7
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3P GAIN MUTATED                         1                       0
  3P GAIN WILD-TYPE                       0                       5
D5V28, multiclass
                                     clus
vv                                    3P GAIN MUTATED 3P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           2                 7
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           0                 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)
  3P GAIN MUTATED                                               1
  3P GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  3P GAIN MUTATED                                                1
  3P GAIN WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3P GAIN MUTATED                                                                                  13
  3P GAIN WILD-TYPE                                                                                41
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3P GAIN MUTATED                                                                                             21
  3P GAIN WILD-TYPE                                                                                           56
D5V29, multiclass
                                                                                              clus
vv                                                                                             3P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  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)              21
                                                                                              clus
vv                                                                                             3P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           41
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                56
[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"
D5V30, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    9 17
  3P GAIN WILD-TYPE 45 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9   17
  3P GAIN WILD-TYPE   45   42
         clus
vv        3P GAIN MUTATED 3P GAIN WILD-TYPE
  ABSENT                9                45
  PRESENT              17                42
[1] 2 2
[1] FALSE
D5V31, continuous
D5V32, continuous
D5V33, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   10 21
  3P GAIN WILD-TYPE 25 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     10   21
  3P GAIN WILD-TYPE   25   60
                                          clus
vv                                         3P GAIN MUTATED 3P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  10                25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              21                60
[1] 2 2
[1] FALSE
D5V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  3P GAIN MUTATED       0                   27                   2
  3P GAIN WILD-TYPE     3                   86                   3
D5V35, multiclass
                      clus
vv                     3P GAIN MUTATED 3P GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              27                86
  SIMPLE HYSTERECTOMY                2                 3
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3P GAIN MUTATED              2          10         11
  3P GAIN WILD-TYPE            6          30         29
D5V36, multiclass
              clus
vv             3P GAIN MUTATED 3P GAIN WILD-TYPE
  CURRENT USER               2                 6
  FORMER USER               10                30
  NEVER USED                11                29
[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, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   13  4
  3P GAIN WILD-TYPE 60 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     13    4
  3P GAIN WILD-TYPE   60   10
         clus
vv        3P GAIN MUTATED 3P GAIN WILD-TYPE
  ABSENT               13                60
  PRESENT               4                10
[1] 2 2
[1] FALSE
D5V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  3P GAIN MUTATED     0    0   6   12    4  1   1    1    1   4   1  1  0
  3P GAIN WILD-TYPE   2    1  16   39   17  2   5    5    7   9   1  0  7
D5V40, multiclass
      clus
vv     3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                6                16
  T1B1              12                39
  T1B2               4                17
  T2                 1                 2
  T2A                1                 5
  T2A1               1                 5
  T2A2               1                 7
  T2B                4                 9
  T3B                1                 1
  T4                 1                 0
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V41, continuous

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   78 22
  3Q GAIN WILD-TYPE 59 10
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              100                69 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               22                10 
$`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-A1BL TCGA-C5-A1BM TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29        82.85        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-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX 
        2.43        40.93         3.58        44.22        73.18        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A7CJ TCGA-C5-A7CK 
       78.35       100.14        18.02        17.85       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL 
       15.48        85.55        94.95         9.34         2.73        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76         2.66       117.99       118.65        22.98        16.83 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        7.33         8.28         0.76        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A50E TCGA-EA-A5FO 
        0.82         0.62        13.05        14.50         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EK-A2GZ TCGA-EK-A2PG 
       13.91         0.69        14.99        14.96        12.59         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.59         0.07         4.04        23.70         2.24         0.10 
TCGA-EK-A2RO TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A3NI 
        0.07        20.35         6.94         4.47        23.84         1.45 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-HG-A2PA 
        1.48         0.82         3.52         1.35         1.97        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LL 
       21.67        20.78        14.93       137.16       117.40        36.36 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU TCGA-MU-A51Y 
       19.33        20.48        15.58         5.13         0.10        13.87 
TCGA-MU-A8JM TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        5.42         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DW TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        5.75         3.88        11.67        93.99 

$`3Q GAIN WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A2LV 
       57.04        68.84        18.74         5.46        19.86        73.45 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
       38.43         0.82        52.01        20.42       182.93        25.35 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-DR-A0ZM 
        9.67        73.41        17.19        60.69        13.61        58.88 
TCGA-DS-A7WF TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       16.18         1.18        14.50         1.35         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
       12.66        12.82        14.89        13.58        13.48        45.96 
TCGA-EK-A2IP TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A3GJ TCGA-EK-A3GK 
        6.64         0.03         0.36         1.18         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG 
        0.03         7.92        14.70         6.12         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A57G TCGA-FU-A770 
        2.17         0.66         1.02         1.58         1.32         1.12 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
        4.11       147.39        66.81        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A69B TCGA-LP-A4AW TCGA-LP-A4AX 
       26.56        14.43        16.64        10.06         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV 
        0.82         0.03        29.72         0.07         4.34         3.72 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        4.80         6.25        19.59 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           177.04            182.93 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           14.945            10.060 
[1] "0.1 - 177.0 (14.9)" "0.0 - 182.9 (10.1)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                T1 T2+T3+T4
  3Q GAIN MUTATED   55       24
  3Q GAIN WILD-TYPE 42       15
D6V3, multiclass
          clus
vv         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                    55                42
  T2+T3+T4              24                15
[1] 2 2
[1] FALSE
D6V4, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   45 30
  3Q GAIN WILD-TYPE 42 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     45   30
  3Q GAIN WILD-TYPE   42   10
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              45                42
  1              30                10
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED   46  0 37
  3Q GAIN WILD-TYPE 26  3 28
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              46                26
  M1               0                 3
  MX              37                28
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED               0                               92
  3Q GAIN WILD-TYPE             2                               52
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3Q GAIN MUTATED                                               1
  3Q GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3Q GAIN MUTATED                                     7
  3Q GAIN WILD-TYPE                                  13
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3Q GAIN MUTATED                                           1
  3Q GAIN WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3Q GAIN MUTATED                                              3
  3Q GAIN WILD-TYPE                                            1
D6V6, multiclass
                                               clus
vv                                              3Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           92
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                3
                                               clus
vv                                              3Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                             52
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  1
[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"
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   22 82
  3Q GAIN WILD-TYPE  5 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     22   82
  3Q GAIN WILD-TYPE    5   67
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               22                 5
  YES              82                67
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  4     9
  3Q GAIN WILD-TYPE                                3     6
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED                          12
  3Q GAIN WILD-TYPE                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           0    75
  3Q GAIN WILD-TYPE                                         1    55
D6V10, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        4                 3
  ASIAN                                                   9                 6
  BLACK OR AFRICAN AMERICAN                              12                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  75                55
[1] 5 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    5 77
  3Q GAIN WILD-TYPE  6 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5   77
  3Q GAIN WILD-TYPE    6   50
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 6
  NOT HISPANIC OR LATINO              77                50
[1] 2 2
[1] FALSE
D6V12, continuous
D6V13, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   32 14
  3Q GAIN WILD-TYPE 16  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     32   14
  3Q GAIN WILD-TYPE   16    5
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  TUMOR FREE              32                16
  WITH TUMOR              14                 5
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  3Q GAIN MUTATED         1      6       2            88       7
  3Q GAIN WILD-TYPE       0      4       4            59       5
D6V14, multiclass
               clus
vv              3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      6                 4
  UKRAINE                     2                 4
  UNITED STATES              88                59
  VIETNAM                     7                 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                G1 G2 G3 G4 GX
  3Q GAIN MUTATED    7 53 41  0  3
  3Q GAIN WILD-TYPE  7 30 31  1  2
D6V15, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  G1               7                 7
  G2              53                30
  G3              41                31
  G4               0                 1
  GX               3                 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"
D6V16, continuous
D6V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3Q GAIN MUTATED                                            13
  3Q GAIN WILD-TYPE                                           8
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  3Q GAIN MUTATED                                        4
  3Q GAIN WILD-TYPE                                      4
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  3Q GAIN MUTATED                                                 1
  3Q GAIN WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3Q GAIN MUTATED               23                  50
  3Q GAIN WILD-TYPE             13                  33
D6V18, multiclass
                                                 clus
vv                                                3Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                  13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                               23
  LIFELONG NON-SMOKER                                          50
                                                 clus
vv                                                3Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     8
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 13
  LIFELONG NON-SMOKER                                            33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  3Q GAIN MUTATED            14       20             9        3
  3Q GAIN WILD-TYPE           3       17             2        2
D6V20, multiclass
               clus
vv              3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COMBINATION                14                 3
  EXTERNAL                   20                17
  EXTERNAL BEAM               9                 2
  INTERNAL                    3                 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"
D6V21, binary
                   cls
clus                0 1
  3Q GAIN MUTATED   5 2
  3Q GAIN WILD-TYPE 6 1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5    2
  3Q GAIN WILD-TYPE    6    1
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CGY               5                 6
  GY                2                 1
[1] 2 2
[1] FALSE
D6V22, continuous
D6V23, continuous
D6V24, continuous
D6V25, continuous
D6V26, continuous
D6V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  3Q GAIN MUTATED                                     1
  3Q GAIN WILD-TYPE                                   1
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  3Q GAIN MUTATED                                     4                       7
  3Q GAIN WILD-TYPE                                   2                       2
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3Q GAIN MUTATED                         1                       3
  3Q GAIN WILD-TYPE                       0                       2
D6V28, multiclass
                                     clus
vv                                    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               4                 2
  OTHER LOCATION, SPECIFY                           7                 2
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           3                 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                                                3
  3Q GAIN WILD-TYPE                                              7
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3Q GAIN MUTATED                                                                                  34
  3Q GAIN WILD-TYPE                                                                                20
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3Q GAIN MUTATED                                                                                             47
  3Q GAIN WILD-TYPE                                                                                           30
D6V29, multiclass
                                                                                              clus
vv                                                                                             3Q GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             3
  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)              47
                                                                                              clus
vv                                                                                             3Q GAIN WILD-TYPE
  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)                           20
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                30
[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"
D6V30, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   28 38
  3Q GAIN WILD-TYPE 26 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     28   38
  3Q GAIN WILD-TYPE   26   21
         clus
vv        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ABSENT               28                26
  PRESENT              38                21
[1] 2 2
[1] FALSE
D6V31, continuous
D6V32, continuous
D6V33, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   24 49
  3Q GAIN WILD-TYPE 11 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     24   49
  3Q GAIN WILD-TYPE   11   32
                                          clus
vv                                         3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  24                11
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              49                32
[1] 2 2
[1] FALSE
D6V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  3Q GAIN MUTATED       0                   69                   2
  3Q GAIN WILD-TYPE     3                   44                   3
D6V35, multiclass
                      clus
vv                     3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              69                44
  SIMPLE HYSTERECTOMY                2                 3
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3Q GAIN MUTATED              5          24         21
  3Q GAIN WILD-TYPE            3          16         19
D6V36, multiclass
              clus
vv             3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CURRENT USER               5                 3
  FORMER USER               24                16
  NEVER USED                21                19
[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, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   42  9
  3Q GAIN WILD-TYPE 31  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     42    9
  3Q GAIN WILD-TYPE   31    5
         clus
vv        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ABSENT               42                31
  PRESENT               9                 5
[1] 2 2
[1] FALSE
D6V39, continuous
[1] "Remove cluster labels:" "3Q GAIN WILD-TYPE"     
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                 1 
     TCGA-C5-A1MH      TCGA-C5-A1MN      TCGA-C5-A1MP      TCGA-EK-A2RO 
"3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" 
     TCGA-HM-A3JK      TCGA-JW-A852      TCGA-MU-A51Y      TCGA-MU-A8JM 
"3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  3Q GAIN MUTATED     0    0  14   29   12  3   4    5    2   7   2  1  4
  3Q GAIN WILD-TYPE   2    1   8   22    9  0   2    1    6   6   0  0  3
D6V40, multiclass
      clus
vv     3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B               14                 8
  T1B1              29                22
  T1B2              12                 9
  T2                 3                 0
  T2A                4                 2
  T2A1               5                 1
  T2A2               2                 6
  T2B                7                 6
  T3B                2                 0
  T4                 1                 0
  TX                 4                 3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V41, continuous

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     3   2
  4P GAIN WILD-TYPE 134  30
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               164 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                30 
$`4P GAIN MUTATED`
TCGA-C5-A1MN TCGA-C5-A7X5 TCGA-FU-A23K TCGA-IR-A3LF TCGA-R2-A69V 
       40.93        13.61         1.22        96.95        19.59 

$`4P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-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         0.82        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       182.93        25.35       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
        9.67        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        9.34         2.73        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50         1.81        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH 
        4.11       147.39       137.16        66.81       117.40        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 
        3.39         3.72         5.75         4.80         6.25         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             1.22              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            96.95            182.93 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           19.590            13.265 
[1] "1.2 - 97.0 (19.6)"  "0.0 - 182.9 (13.3)"
[1] "hr=" "1.7"
D7V2, continuous
                   vv
clus                T1 T2+T3+T4
  4P GAIN MUTATED    3        0
  4P GAIN WILD-TYPE 94       39
D7V3, multiclass
          clus
vv         4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1                     3                94
  T2+T3+T4               0                39
[1] 2 2
[1] FALSE
D7V4, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 85 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    1
  4P GAIN WILD-TYPE   85   39
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               2                85
  1               1                39
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4P GAIN MUTATED    2  0  1
  4P GAIN WILD-TYPE 70  3 64
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               2                70
  M1               0                 3
  MX               1                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED               0                                5
  4P GAIN WILD-TYPE             2                              139
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4P GAIN MUTATED                                               1
  4P GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4P GAIN MUTATED                                     0
  4P GAIN WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4P GAIN MUTATED                                           0
  4P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4P GAIN MUTATED                                              0
  4P GAIN WILD-TYPE                                            4
D7V6, multiclass
                                               clus
vv                                              4P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            5
  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                                              4P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            139
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1   5
  4P GAIN WILD-TYPE  26 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    5
  4P GAIN WILD-TYPE   26  144
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                26
  YES               5               144
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                52 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-DR-A0ZM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A5YI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     0
  4P GAIN WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED                           1
  4P GAIN WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0     5
  4P GAIN WILD-TYPE                                         1   125
D7V10, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   0                15
  BLACK OR AFRICAN AMERICAN                               1                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               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"
D7V11, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   3
  4P GAIN WILD-TYPE  11 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    3
  4P GAIN WILD-TYPE   11  124
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               3               124
[1] 2 2
[1] FALSE
D7V12, continuous
D7V13, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  0
  4P GAIN WILD-TYPE 47 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    0
  4P GAIN WILD-TYPE   47   19
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  TUMOR FREE               1                47
  WITH TUMOR               0                19
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  4P GAIN MUTATED         0      0       0             6       0
  4P GAIN WILD-TYPE       1     10       6           141      12
D7V14, multiclass
               clus
vv              4P GAIN MUTATED 4P GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 6
  UNITED STATES               6               141
  VIETNAM                     0                12
[1] 5 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                G1 G2 G3 G4 GX
  4P GAIN MUTATED    0  3  3  0  0
  4P GAIN WILD-TYPE 14 80 69  1  5
D7V15, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  G1               0                14
  G2               3                80
  G3               3                69
  G4               0                 1
  GX               0                 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"
D7V16, continuous
D7V17, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                52 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-DR-A0ZM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A5YI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4P GAIN MUTATED                                             0
  4P GAIN WILD-TYPE                                          21
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  4P GAIN MUTATED                                        0
  4P GAIN WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  4P GAIN MUTATED                                                 0
  4P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4P GAIN MUTATED                1                   3
  4P GAIN WILD-TYPE             35                  80
D7V18, multiclass
                                                 clus
vv                                                4P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                1
  LIFELONG NON-SMOKER                                           3
                                                 clus
vv                                                4P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 35
  LIFELONG NON-SMOKER                                            80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  4P GAIN MUTATED             1        3             0        0
  4P GAIN WILD-TYPE          16       34            11        5
D7V20, multiclass
               clus
vv              4P GAIN MUTATED 4P GAIN WILD-TYPE
  COMBINATION                 1                16
  EXTERNAL                    3                34
  EXTERNAL BEAM               0                11
  INTERNAL                    0                 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"
D7V21, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  1
  4P GAIN WILD-TYPE 10  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    1
  4P GAIN WILD-TYPE   10    2
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  CGY               1                10
  GY                1                 2
[1] 2 2
[1] FALSE
D7V22, continuous
D7V23, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                91 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BE        TCGA-C5-A1BI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI        TCGA-C5-A1MJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        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-A2LY        TCGA-C5-A2LZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-C5-A7X8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A411        TCGA-EA-A44S 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EX-A449        TCGA-FU-A2QG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3TQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JK        TCGA-IR-A3L7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LC        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-JW-A5VG        TCGA-JW-A5VI        TCGA-JW-A5VJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-JW-A5VL        TCGA-JW-A69B        TCGA-JW-A852 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V24, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2               103 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BE        TCGA-C5-A1BF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BM        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1M6        TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MJ        TCGA-C5-A1MK        TCGA-C5-A1MP        TCGA-C5-A2LS 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A3HE        TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7CH        TCGA-C5-A7CJ        TCGA-C5-A7CK        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-A7UH        TCGA-C5-A7UI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7X3        TCGA-C5-A7X8        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH        TCGA-DS-A7WI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A411        TCGA-EA-A44S 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EA-A5ZD        TCGA-EK-A2IP 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EK-A2RK        TCGA-EX-A69L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3TQ        TCGA-FU-A3YQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A57G        TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3L7        TCGA-IR-A3LC        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-IR-A3LL        TCGA-JW-A5VG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A5VL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-A69B        TCGA-JW-A852        TCGA-MU-A8JM        TCGA-PN-A8MA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V25, continuous
D7V26, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                98 
       TCGA-BI-A0VS        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI        TCGA-C5-A1MJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        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-A2LY        TCGA-C5-A2LZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-C5-A7X8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A3QE        TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A411 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A44S        TCGA-EA-A4BA        TCGA-EA-A556        TCGA-EA-A5O9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A6QX        TCGA-EK-A2RN        TCGA-EX-A1H6        TCGA-EX-A449 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-IR-A3L7        TCGA-IR-A3LC        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-IR-A3LL        TCGA-JW-A5VG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A5VL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-A69B        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-RA-A741 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V27, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                92 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BE        TCGA-C5-A1BI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI        TCGA-C5-A1MJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        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-A2LY        TCGA-C5-A2LZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-C5-A7X8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A411        TCGA-EA-A44S 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EX-A69M        TCGA-FU-A2QG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3TQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LC        TCGA-IR-A3LH        TCGA-IR-A3LI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LK        TCGA-IR-A3LL        TCGA-JW-A5VG        TCGA-JW-A5VI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A5VL        TCGA-JW-A69B 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-A852        TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  4P GAIN MUTATED                                     0
  4P GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  4P GAIN MUTATED                                     0                       0
  4P GAIN WILD-TYPE                                   6                       9
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4P GAIN MUTATED                         0                       0
  4P GAIN WILD-TYPE                       1                       5
D7V28, multiclass
                   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                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4P GAIN MUTATED                                                                                   1
  4P GAIN WILD-TYPE                                                                                53
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4P GAIN MUTATED                                                                                              2
  4P GAIN WILD-TYPE                                                                                           75
D7V29, 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)                          1
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               2
                                                                                              clus
vv                                                                                             4P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                75
[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"
D7V30, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  2
  4P GAIN WILD-TYPE 53 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    2
  4P GAIN WILD-TYPE   53   57
         clus
vv        4P GAIN MUTATED 4P GAIN WILD-TYPE
  ABSENT                1                53
  PRESENT               2                57
[1] 2 2
[1] FALSE
D7V31, continuous
D7V32, continuous
D7V33, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  2
  4P GAIN WILD-TYPE 33 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    2
  4P GAIN WILD-TYPE   33   79
                                          clus
vv                                         4P GAIN MUTATED 4P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   2                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               2                79
[1] 2 2
[1] FALSE
D7V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  4P GAIN MUTATED       0                    2                   1
  4P GAIN WILD-TYPE     3                  111                   4
D7V35, multiclass
                      clus
vv                     4P GAIN MUTATED 4P GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY               2               111
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4P GAIN MUTATED              0           1          1
  4P GAIN WILD-TYPE            8          39         39
D7V36, multiclass
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                86 
       TCGA-C5-A1BI        TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1M6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A2LY        TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7UH        TCGA-C5-A7X3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-DS-A7WF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DS-A7WH        TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A3HQ        TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A3QD        TCGA-EA-A3QE        TCGA-EA-A410        TCGA-EA-A411 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EA-A44S        TCGA-EA-A4BA        TCGA-EA-A50E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EA-A5ZE        TCGA-EA-A5ZF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EK-A2R7        TCGA-EK-A3GK        TCGA-EX-A1H5        TCGA-EX-A1H6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-EX-A69L        TCGA-EX-A69M        TCGA-FU-A2QG 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FU-A57G        TCGA-FU-A770        TCGA-HM-A3JJ        TCGA-HM-A3JK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LC        TCGA-IR-A3LH        TCGA-IR-A3LI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IR-A3LK        TCGA-JW-A5VG        TCGA-JW-A5VI        TCGA-JW-A5VJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-JW-A69B        TCGA-LP-A5U3        TCGA-PN-A8MA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-Q1-A5R1        TCGA-Q1-A5R2        TCGA-Q1-A5R3        TCGA-Q1-A6DV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-Q1-A73P        TCGA-UC-A7PD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V37, continuous
D7V38, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  0
  4P GAIN WILD-TYPE 71 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    0
  4P GAIN WILD-TYPE   71   14
         clus
vv        4P GAIN MUTATED 4P GAIN WILD-TYPE
  ABSENT                2                71
  PRESENT               0                14
[1] 2 2
[1] FALSE
D7V39, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                 8 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1MP        TCGA-EK-A2RO 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  4P GAIN MUTATED     0    0   1    2    0  0   0    0    0   0   0  0  0
  4P GAIN WILD-TYPE   2    1  21   49   21  3   6    6    8  13   2  1  7
D7V40, multiclass
      clus
vv     4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                1                21
  T1B1               2                49
  T1B2               0                21
  T2                 0                 3
  T2A                0                 6
  T2A1               0                 6
  T2A2               0                 8
  T2B                0                13
  T3B                0                 2
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V41, continuous

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     6   0
  4Q GAIN WILD-TYPE 131  32
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               163 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                32 
$`4Q GAIN MUTATED`
TCGA-C5-A1MP TCGA-EK-A3GK TCGA-FU-A23K TCGA-IR-A3LF TCGA-MY-A5BF TCGA-R2-A69V 
        3.58         0.10         1.22        96.95         4.34        19.59 

$`4Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       40.93        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         0.82        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       182.93        25.35       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
        9.67        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        9.34        13.61         2.73        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
        2.66       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        7.33         8.28         0.76        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35        14.50         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.58        13.48        12.59        45.96         6.64         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.59         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
       23.70         2.24         0.10         0.07         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH 
        4.11       147.39       137.16        66.81       117.40        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.07         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD 
        3.72         5.75         4.80         6.25         3.88        11.67 
TCGA-UC-A7PF 
       93.99 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.10              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            96.95            182.93 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3.96             13.61 
[1] "0.1 - 97.0 (4.0)"   "0.0 - 182.9 (13.6)"
[1] "hr="     "2.5e+07"
D8V2, continuous
                   vv
clus                T1 T2+T3+T4
  4Q GAIN MUTATED    5        1
  4Q GAIN WILD-TYPE 92       38
D8V3, multiclass
          clus
vv         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1                     5                92
  T2+T3+T4               1                38
[1] 2 2
[1] FALSE
D8V4, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    4  2
  4Q GAIN WILD-TYPE 83 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    2
  4Q GAIN WILD-TYPE   83   38
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               4                83
  1               2                38
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4Q GAIN MUTATED    2  0  4
  4Q GAIN WILD-TYPE 70  3 61
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               2                70
  M1               0                 3
  MX               4                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED               0                                5
  4Q GAIN WILD-TYPE             2                              139
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4Q GAIN MUTATED                                               1
  4Q GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4Q GAIN MUTATED                                     1
  4Q GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4Q GAIN MUTATED                                           0
  4Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4Q GAIN MUTATED                                              0
  4Q GAIN WILD-TYPE                                            4
D8V6, multiclass
                                               clus
vv                                              4Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            5
  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                                              4Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            139
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   7
  4Q GAIN WILD-TYPE  27 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    7
  4Q GAIN WILD-TYPE   27  142
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                27
  YES               7               142
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED                           1
  4Q GAIN WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0     6
  4Q GAIN WILD-TYPE                                         1   124
D8V10, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   0                15
  BLACK OR AFRICAN AMERICAN                               1                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   6               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"
D8V11, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   4
  4Q GAIN WILD-TYPE  11 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    4
  4Q GAIN WILD-TYPE   11  123
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               4               123
[1] 2 2
[1] FALSE
D8V12, continuous
D8V13, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    1  0
  4Q GAIN WILD-TYPE 47 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    0
  4Q GAIN WILD-TYPE   47   19
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  TUMOR FREE               1                47
  WITH TUMOR               0                19
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  4Q GAIN MUTATED         0      0       0             7       0
  4Q GAIN WILD-TYPE       1     10       6           140      12
D8V14, multiclass
               clus
vv              4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 6
  UNITED STATES               7               140
  VIETNAM                     0                12
[1] 5 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                G1 G2 G3 G4 GX
  4Q GAIN MUTATED    1  2  4  0  0
  4Q GAIN WILD-TYPE 13 81 68  1  5
D8V15, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  G1               1                13
  G2               2                81
  G3               4                68
  G4               0                 1
  GX               0                 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"
D8V16, continuous
D8V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4Q GAIN MUTATED                                             0
  4Q GAIN WILD-TYPE                                          21
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  4Q GAIN MUTATED                                        0
  4Q GAIN WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  4Q GAIN MUTATED                                                 0
  4Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4Q GAIN MUTATED                0                   5
  4Q GAIN WILD-TYPE             36                  78
D8V18, multiclass
                                                 clus
vv                                                4Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                0
  LIFELONG NON-SMOKER                                           5
                                                 clus
vv                                                4Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 36
  LIFELONG NON-SMOKER                                            78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  4Q GAIN MUTATED             0        2             0        0
  4Q GAIN WILD-TYPE          17       35            11        5
D8V20, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                68 
       TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BF        TCGA-C5-A1BI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BL        TCGA-C5-A1BM        TCGA-C5-A1BN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6        TCGA-C5-A1M8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1M9        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LT        TCGA-C5-A2LX 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2LY        TCGA-C5-A2LZ        TCGA-C5-A3HE        TCGA-C5-A3HF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A3HL        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7X5        TCGA-C5-A7X8        TCGA-DR-A0ZM        TCGA-DS-A0VK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-DS-A5RQ        TCGA-DS-A7WH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A3QD        TCGA-EA-A3Y4        TCGA-EA-A44S 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A4BA        TCGA-EA-A5O9        TCGA-EX-A3L1        TCGA-EX-A449 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LC        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-JW-A5VG        TCGA-JW-A5VI        TCGA-PN-A8MA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-Q1-A5R2        TCGA-Q1-A5R3        TCGA-RA-A741        TCGA-UC-A7PD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V21, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    1  1
  4Q GAIN WILD-TYPE 10  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    1
  4Q GAIN WILD-TYPE   10    2
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  CGY               1                10
  GY                1                 2
[1] 2 2
[1] FALSE
D8V22, continuous
D8V23, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                91 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BE        TCGA-C5-A1BI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI        TCGA-C5-A1MJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2LZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-C5-A7X8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A411        TCGA-EA-A44S 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EX-A449        TCGA-FU-A2QG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3TQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JK        TCGA-IR-A3L7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LC        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-JW-A5VG        TCGA-JW-A5VI        TCGA-JW-A5VJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-JW-A5VL        TCGA-JW-A69B        TCGA-JW-A852 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V24, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               103 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BE        TCGA-C5-A1BF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BM        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1M6        TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1MJ        TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A3HE        TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7CH        TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7UI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7X3        TCGA-C5-A7X8        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH        TCGA-DS-A7WI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A411        TCGA-EA-A44S 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EA-A5ZD        TCGA-EK-A2IP 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EK-A2RK        TCGA-EX-A69L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3TQ        TCGA-FU-A3YQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A57G        TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3L7        TCGA-IR-A3LC        TCGA-IR-A3LH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LI        TCGA-IR-A3LK        TCGA-IR-A3LL        TCGA-JW-A5VG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A5VL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-A69B        TCGA-JW-A852        TCGA-MU-A8JM        TCGA-PN-A8MA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V25, continuous
D8V26, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                98 
       TCGA-BI-A0VS        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI        TCGA-C5-A1MJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2LZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-C5-A7X8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A3QE        TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A411 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A44S        TCGA-EA-A4BA        TCGA-EA-A556        TCGA-EA-A5O9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A6QX        TCGA-EK-A2RN        TCGA-EX-A1H6        TCGA-EX-A449 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-IR-A3L7        TCGA-IR-A3LC        TCGA-IR-A3LH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LI        TCGA-IR-A3LK        TCGA-IR-A3LL        TCGA-JW-A5VG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A5VL 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-A69B        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-RA-A741 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V27, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                92 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BE        TCGA-C5-A1BI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI        TCGA-C5-A1MJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2LZ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7CH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-C5-A7X8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A411        TCGA-EA-A44S 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EX-A69M        TCGA-FU-A2QG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3TQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LC        TCGA-IR-A3LH        TCGA-IR-A3LI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LK        TCGA-IR-A3LL        TCGA-JW-A5VG        TCGA-JW-A5VI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A5VL        TCGA-JW-A69B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-A852        TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  4Q GAIN MUTATED                                     0
  4Q GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  4Q GAIN MUTATED                                     0                       0
  4Q GAIN WILD-TYPE                                   6                       9
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4Q GAIN MUTATED                         0                       0
  4Q GAIN WILD-TYPE                       1                       5
D8V28, multiclass
                   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                                                1
  4Q GAIN WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4Q GAIN MUTATED                                                                                   2
  4Q GAIN WILD-TYPE                                                                                52
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4Q GAIN MUTATED                                                                                              2
  4Q GAIN WILD-TYPE                                                                                           75
D8V29, multiclass
                                                                                              clus
vv                                                                                             4Q 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)               2
                                                                                              clus
vv                                                                                             4Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                75
[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"
D8V30, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    1  5
  4Q GAIN WILD-TYPE 53 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    5
  4Q GAIN WILD-TYPE   53   54
         clus
vv        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ABSENT                1                53
  PRESENT               5                54
[1] 2 2
[1] FALSE
D8V31, continuous
D8V32, continuous
D8V33, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  2
  4Q GAIN WILD-TYPE 35 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    2
  4Q GAIN WILD-TYPE   35   79
                                          clus
vv                                         4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   0                35
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               2                79
[1] 2 2
[1] FALSE
D8V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  4Q GAIN MUTATED       1                    4                   1
  4Q GAIN WILD-TYPE     2                  109                   4
D8V35, multiclass
                      clus
vv                     4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  OTHER                              1                 2
  RADICAL HYSTERECTOMY               4               109
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4Q GAIN MUTATED              1           0          1
  4Q GAIN WILD-TYPE            7          40         39
D8V36, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                86 
       TCGA-C5-A1BI        TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1M6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MN        TCGA-C5-A2LT        TCGA-C5-A2LV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2M1        TCGA-C5-A2M2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7UH 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-C5-A7X3        TCGA-DR-A0ZL        TCGA-DR-A0ZM        TCGA-DS-A0VK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A3LQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DS-A7WF        TCGA-DS-A7WH        TCGA-DS-A7WI        TCGA-EA-A1QS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR        TCGA-EA-A3HS 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE        TCGA-EA-A410 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A411        TCGA-EA-A43B        TCGA-EA-A44S        TCGA-EA-A4BA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A50E        TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EA-A5ZE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EA-A5ZF        TCGA-EK-A2R7        TCGA-EX-A1H5        TCGA-EX-A1H6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-EX-A69L        TCGA-EX-A69M        TCGA-FU-A2QG 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FU-A57G        TCGA-FU-A770        TCGA-HM-A3JJ        TCGA-HM-A3JK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LC        TCGA-IR-A3LH        TCGA-IR-A3LI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IR-A3LK        TCGA-JW-A5VG        TCGA-JW-A5VI        TCGA-JW-A5VJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-JW-A69B        TCGA-LP-A5U3        TCGA-PN-A8MA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-Q1-A5R1        TCGA-Q1-A5R2        TCGA-Q1-A5R3        TCGA-Q1-A6DV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-Q1-A73P        TCGA-UC-A7PD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V37, continuous
D8V38, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    3  0
  4Q GAIN WILD-TYPE 70 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    0
  4Q GAIN WILD-TYPE   70   14
         clus
vv        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ABSENT                3                70
  PRESENT               0                14
[1] 2 2
[1] FALSE
D8V39, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                 8 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1MN        TCGA-EK-A2RO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  4Q GAIN MUTATED     0    0   1    3    1  0   0    0    1   0   0  0  0
  4Q GAIN WILD-TYPE   2    1  21   48   20  3   6    6    7  13   2  1  7
D8V40, multiclass
      clus
vv     4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                1                21
  T1B1               3                48
  T1B2               1                20
  T2                 0                 3
  T2A                0                 6
  T2A1               0                 6
  T2A2               1                 7
  T2B                0                13
  T3B                0                 2
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V41, continuous

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   47  8
  5P GAIN WILD-TYPE 90 24
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               55               114 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8                24 
$`5P GAIN MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BJ TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1M7 
       49.48        57.04       144.16        19.86        31.40        46.32 
TCGA-C5-A1ME TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LZ TCGA-C5-A2M1 
       57.73        40.93         3.58        73.18       100.14        38.43 
TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE 
       52.01        18.02        15.48         9.67        73.41        85.55 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A3HR 
       60.69         9.34         2.73        22.98         0.76         1.32 
TCGA-EA-A3Y4 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2PG 
       14.50        14.50         1.81        13.91        14.96         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.59         1.18         0.10         0.10         0.03        20.35 
TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI TCGA-FU-A5XV 
        6.94         4.47        23.84         0.66         1.45         1.97 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       25.41        21.67        78.71        26.56        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A852 TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       16.64         5.13         0.07         2.96         3.45         5.85 
TCGA-Q1-A6DT 
        3.39 

$`5P GAIN WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK 
       23.67        11.44        68.84        18.74        36.56       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 
      173.29        82.85         5.46        67.46        30.21        35.01 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A2LS 
       53.16        38.99        35.61         0.46         2.43        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M2 TCGA-C5-A3HF TCGA-C5-A3HL 
       73.45        83.05        78.35         0.82        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7UC TCGA-C5-A7UI 
      182.93        25.35       101.82       134.33        17.19        94.95 
TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       13.61        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT 
      118.65        16.83        16.18         7.33         8.28        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 
        1.74         0.82         0.62        13.05         1.18         1.35 
TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.35        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
        0.69        14.99        13.58        13.48        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        6.64         0.07         4.04         0.03         0.36        23.70 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M 
        2.24         0.07         0.10         7.92        14.70         6.12 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        1.22         0.92         2.17         1.02         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A3JK 
        0.82         3.52         1.35         1.32         1.12        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       96.95        81.96        19.33        20.48        15.58        10.06 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        0.10         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        5.42        29.72         4.34         3.72         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           144.16            182.93 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            14.50             12.74 
[1] "0.0 - 144.2 (14.5)" "0.0 - 182.9 (12.7)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                T1 T2+T3+T4
  5P GAIN MUTATED   25       14
  5P GAIN WILD-TYPE 72       25
D9V3, multiclass
          clus
vv         5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                    25                72
  T2+T3+T4              14                25
[1] 2 2
[1] FALSE
D9V4, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   24 12
  5P GAIN WILD-TYPE 63 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     24   12
  5P GAIN WILD-TYPE   63   28
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              24                63
  1              12                28
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED   23  0 19
  5P GAIN WILD-TYPE 49  3 46
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              23                49
  M1               0                 3
  MX              19                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED               0                               55
  5P GAIN WILD-TYPE             2                               89
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5P GAIN MUTATED                                               1
  5P GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5P GAIN MUTATED                                     4
  5P GAIN WILD-TYPE                                  16
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5P GAIN MUTATED                                           0
  5P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5P GAIN MUTATED                                              1
  5P GAIN WILD-TYPE                                            3
D9V6, multiclass
                                               clus
vv                                              5P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           55
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              5P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                             89
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    7 54
  5P GAIN WILD-TYPE 20 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   54
  5P GAIN WILD-TYPE   20   95
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                7                20
  YES              54                95
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  2     4
  5P GAIN WILD-TYPE                                5    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED                           7
  5P GAIN WILD-TYPE                        11
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           0    47
  5P GAIN WILD-TYPE                                         1    83
D9V10, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 5
  ASIAN                                                   4                11
  BLACK OR AFRICAN AMERICAN                               7                11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  47                83
[1] 5 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    5 42
  5P GAIN WILD-TYPE  6 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5   42
  5P GAIN WILD-TYPE    6   85
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 6
  NOT HISPANIC OR LATINO              42                85
[1] 2 2
[1] FALSE
D9V12, continuous
D9V13, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   17  5
  5P GAIN WILD-TYPE 31 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     17    5
  5P GAIN WILD-TYPE   31   14
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  TUMOR FREE              17                31
  WITH TUMOR               5                14
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  5P GAIN MUTATED         1      2       3            52       3
  5P GAIN WILD-TYPE       0      8       3            95       9
D9V14, multiclass
               clus
vv              5P GAIN MUTATED 5P GAIN WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      2                 8
  UKRAINE                     3                 3
  UNITED STATES              52                95
  VIETNAM                     3                 9
[1] 5 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                G1 G2 G3 G4 GX
  5P GAIN MUTATED    1 28 29  1  1
  5P GAIN WILD-TYPE 13 55 43  0  4
D9V15, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  G1               1                13
  G2              28                55
  G3              29                43
  G4               1                 0
  GX               1                 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"
D9V16, continuous
D9V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5P GAIN MUTATED                                             7
  5P GAIN WILD-TYPE                                          14
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  5P GAIN MUTATED                                        2
  5P GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  5P GAIN MUTATED                                                 0
  5P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5P GAIN MUTATED               14                  26
  5P GAIN WILD-TYPE             22                  57
D9V18, multiclass
                                                 clus
vv                                                5P GAIN 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                                               14
  LIFELONG NON-SMOKER                                          26
                                                 clus
vv                                                5P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 22
  LIFELONG NON-SMOKER                                            57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  5P GAIN MUTATED             3       19             3        3
  5P GAIN WILD-TYPE          14       18             8        2
D9V20, multiclass
               clus
vv              5P GAIN MUTATED 5P GAIN WILD-TYPE
  COMBINATION                 3                14
  EXTERNAL                   19                18
  EXTERNAL BEAM               3                 8
  INTERNAL                    3                 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"
D9V21, binary
                   cls
clus                0 1
  5P GAIN MUTATED   7 1
  5P GAIN WILD-TYPE 4 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7    1
  5P GAIN WILD-TYPE    4    2
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  CGY               7                 4
  GY                1                 2
[1] 2 2
[1] FALSE
D9V22, continuous
D9V23, continuous
D9V24, continuous
D9V25, continuous
D9V26, continuous
D9V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  5P GAIN MUTATED                                     0
  5P GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  5P GAIN MUTATED                                     2                       2
  5P GAIN WILD-TYPE                                   4                       7
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5P GAIN MUTATED                         0                       1
  5P GAIN WILD-TYPE                       1                       4
D9V28, multiclass
                                     clus
vv                                    5P GAIN MUTATED 5P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 4
  OTHER LOCATION, SPECIFY                           2                 7
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 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)
  5P GAIN MUTATED                                               0
  5P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5P GAIN MUTATED                                                1
  5P GAIN WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5P GAIN MUTATED                                                                                  19
  5P GAIN WILD-TYPE                                                                                35
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5P GAIN MUTATED                                                                                             26
  5P GAIN WILD-TYPE                                                                                           51
D9V29, multiclass
                                                                                              clus
vv                                                                                             5P 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)                         19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              26
                                                                                              clus
vv                                                                                             5P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                51
[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"
D9V30, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   16 16
  5P GAIN WILD-TYPE 38 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     16   16
  5P GAIN WILD-TYPE   38   43
         clus
vv        5P GAIN MUTATED 5P GAIN WILD-TYPE
  ABSENT               16                38
  PRESENT              16                43
[1] 2 2
[1] FALSE
D9V31, continuous
D9V32, continuous
D9V33, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    9 30
  5P GAIN WILD-TYPE 26 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      9   30
  5P GAIN WILD-TYPE   26   51
                                          clus
vv                                         5P GAIN MUTATED 5P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   9                26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              30                51
[1] 2 2
[1] FALSE
D9V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  5P GAIN MUTATED       0                   32                   1
  5P GAIN WILD-TYPE     3                   81                   4
D9V35, multiclass
                      clus
vv                     5P GAIN MUTATED 5P GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              32                81
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5P GAIN MUTATED              4          15         10
  5P GAIN WILD-TYPE            4          25         30
D9V36, multiclass
              clus
vv             5P GAIN MUTATED 5P GAIN WILD-TYPE
  CURRENT USER               4                 4
  FORMER USER               15                25
  NEVER USED                10                30
[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, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   17  4
  5P GAIN WILD-TYPE 56 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     17    4
  5P GAIN WILD-TYPE   56   10
         clus
vv        5P GAIN MUTATED 5P GAIN WILD-TYPE
  ABSENT               17                56
  PRESENT               4                10
[1] 2 2
[1] FALSE
D9V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  5P GAIN MUTATED     0    0   4   13    8  0   3    4    0   6   1  0  4
  5P GAIN WILD-TYPE   2    1  18   38   13  3   3    2    8   7   1  1  3
D9V40, multiclass
      clus
vv     5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                4                18
  T1B1              13                38
  T1B2               8                13
  T2                 0                 3
  T2A                3                 3
  T2A1               4                 2
  T2A2               0                 8
  T2B                6                 7
  T3B                1                 1
  T4                 0                 1
  TX                 4                 3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V41, continuous

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    22   4
  5Q GAIN WILD-TYPE 115  28
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               26               143 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                28 
$`5Q GAIN MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1MN TCGA-C5-A7CM TCGA-C5-A7CO 
       31.40        46.32        57.73        40.93         9.67        73.41 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-EA-A1QS TCGA-EA-A5O9 TCGA-EK-A2PG 
       60.69         9.34         2.73         0.76        13.91         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RN TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A69L 
        0.59         0.10         0.03        20.35         6.94         4.47 
TCGA-FU-A3HY TCGA-FU-A5XV TCGA-IR-A3LK TCGA-IR-A3LL TCGA-MY-A5BE TCGA-Q1-A5R2 
        0.66         1.97        26.56        36.36         0.07         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        5.85         3.39 

$`5Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH 
       19.86        67.46        30.21        35.01        53.16        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-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         0.82 
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       182.93        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI 
      101.82       134.33        15.48        17.19        85.55        94.95 
TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       13.61        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      118.65        22.98        16.83        16.18         7.33         8.28 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       12.36         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
        1.18        14.50         1.35         1.35        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD 
       12.66        12.82         0.26        14.89         1.48         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        6.64         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H6 
       23.70         2.24         0.07         0.10         0.10         7.92 
TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         6.12         1.22        23.84         0.92         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.35         1.32         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       96.95        78.71        81.96        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        4.34         2.96         3.72         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        19.59         3.88        11.67        93.99 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            73.41            182.93 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            6.395            14.430 
[1] "0.0 - 73.4 (6.4)"   "0.0 - 182.9 (14.4)"
[1] "hr=" "1.3"
D10V2, continuous
                   vv
clus                T1 T2+T3+T4
  5Q GAIN MUTATED   11        4
  5Q GAIN WILD-TYPE 86       35
D10V3, multiclass
          clus
vv         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                    11                86
  T2+T3+T4               4                35
[1] 2 2
[1] FALSE
D10V4, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    9  6
  5Q GAIN WILD-TYPE 78 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      9    6
  5Q GAIN WILD-TYPE   78   34
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               9                78
  1               6                34
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED    9  0  9
  5Q GAIN WILD-TYPE 63  3 56
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               9                63
  M1               0                 3
  MX               9                56
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED               0                               25
  5Q GAIN WILD-TYPE             2                              119
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5Q GAIN MUTATED                                               1
  5Q GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5Q GAIN MUTATED                                     2
  5Q GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5Q GAIN MUTATED                                           0
  5Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5Q GAIN MUTATED                                              1
  5Q GAIN WILD-TYPE                                            3
D10V6, multiclass
                                               clus
vv                                              5Q 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                                              5Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            119
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3  26
  5Q GAIN WILD-TYPE  24 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   26
  5Q GAIN WILD-TYPE   24  123
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                3                24
  YES              26               123
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED                           3
  5Q GAIN WILD-TYPE                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    25
  5Q GAIN WILD-TYPE                                         1   105
D10V10, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   1                14
  BLACK OR AFRICAN AMERICAN                               3                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  25               105
[1] 5 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     2  21
  5Q GAIN WILD-TYPE   9 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2   21
  5Q GAIN WILD-TYPE    9  106
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              21               106
[1] 2 2
[1] FALSE
D10V12, continuous
D10V13, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    6  2
  5Q GAIN WILD-TYPE 42 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      6    2
  5Q GAIN WILD-TYPE   42   17
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  TUMOR FREE               6                42
  WITH TUMOR               2                17
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  5Q GAIN MUTATED         0      1       1            27       0
  5Q GAIN WILD-TYPE       1      9       5           120      12
D10V14, multiclass
               clus
vv              5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     1                 5
  UNITED STATES              27               120
  VIETNAM                     0                12
[1] 5 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                G1 G2 G3 G4 GX
  5Q GAIN MUTATED    1 13 14  0  1
  5Q GAIN WILD-TYPE 13 70 58  1  4
D10V15, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  G1               1                13
  G2              13                70
  G3              14                58
  G4               0                 1
  GX               1                 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"
D10V16, continuous
D10V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5Q GAIN MUTATED                                             2
  5Q GAIN WILD-TYPE                                          19
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  5Q GAIN MUTATED                                        1
  5Q GAIN WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  5Q GAIN MUTATED                                                 0
  5Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5Q GAIN MUTATED                6                  14
  5Q GAIN WILD-TYPE             30                  69
D10V18, multiclass
                                                 clus
vv                                                5Q 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                                                5Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 30
  LIFELONG NON-SMOKER                                            69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  5Q GAIN MUTATED             2        9             0        2
  5Q GAIN WILD-TYPE          15       28            11        3
D10V20, multiclass
               clus
vv              5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COMBINATION                 2                15
  EXTERNAL                    9                28
  EXTERNAL BEAM               0                11
  INTERNAL                    2                 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"
D10V21, binary
                   cls
clus                0 1
  5Q GAIN MUTATED   3 0
  5Q GAIN WILD-TYPE 8 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    0
  5Q GAIN WILD-TYPE    8    3
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CGY               3                 8
  GY                0                 3
[1] 2 2
[1] FALSE
D10V22, continuous
D10V23, continuous
D10V24, continuous
D10V25, continuous
D10V26, continuous
D10V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  5Q GAIN MUTATED                                     0
  5Q GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  5Q GAIN MUTATED                                     2                       1
  5Q GAIN WILD-TYPE                                   4                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5Q GAIN MUTATED                         0                       0
  5Q GAIN WILD-TYPE                       1                       5
D10V28, multiclass
                                     clus
vv                                    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 4
  OTHER LOCATION, SPECIFY                           1                 8
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 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)
  5Q GAIN MUTATED                                               0
  5Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5Q GAIN MUTATED                                                0
  5Q GAIN WILD-TYPE                                             10
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5Q GAIN MUTATED                                                                                  14
  5Q GAIN WILD-TYPE                                                                                40
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5Q GAIN MUTATED                                                                                              9
  5Q GAIN WILD-TYPE                                                                                           68
D10V29, multiclass
                                                                                              clus
vv                                                                                             5Q 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)                         14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               9
                                                                                              clus
vv                                                                                             5Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           40
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                68
[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"
D10V30, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    8  7
  5Q GAIN WILD-TYPE 46 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8    7
  5Q GAIN WILD-TYPE   46   52
         clus
vv        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ABSENT                8                46
  PRESENT               7                52
[1] 2 2
[1] FALSE
D10V31, continuous
D10V32, continuous
D10V33, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3 13
  5Q GAIN WILD-TYPE 32 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   13
  5Q GAIN WILD-TYPE   32   68
                                          clus
vv                                         5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   3                32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              13                68
[1] 2 2
[1] FALSE
D10V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  5Q GAIN MUTATED       0                   13                   0
  5Q GAIN WILD-TYPE     3                  100                   5
D10V35, multiclass
                      clus
vv                     5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              13               100
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5Q GAIN MUTATED              2           7          7
  5Q GAIN WILD-TYPE            6          33         33
D10V36, multiclass
              clus
vv             5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CURRENT USER               2                 6
  FORMER USER                7                33
  NEVER USED                 7                33
[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, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   10  0
  5Q GAIN WILD-TYPE 63 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     10    0
  5Q GAIN WILD-TYPE   63   14
         clus
vv        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ABSENT               10                63
  PRESENT               0                14
[1] 2 2
[1] FALSE
D10V39, continuous
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                 8 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1MP        TCGA-EK-A2RO 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  5Q GAIN MUTATED     0    0   1    6    4  0   1    1    0   2   0  0  4
  5Q GAIN WILD-TYPE   2    1  21   45   17  3   5    5    8  11   2  1  3
D10V40, multiclass
      clus
vv     5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                1                21
  T1B1               6                45
  T1B2               4                17
  T2                 0                 3
  T2A                1                 5
  T2A1               1                 5
  T2A2               0                 8
  T2B                2                11
  T3B                0                 2
  T4                 0                 1
  TX                 4                 3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V41, continuous

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    24   9
  6P GAIN WILD-TYPE 113  23
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               33               136 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                9                23 
$`6P GAIN MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 
       49.48        57.04         5.46        31.40        46.32        35.01 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A2LY TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A7CH 
       38.99        35.61        78.35        52.01        17.85        25.35 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A439 
       85.55        94.95         2.73         8.28         0.76        14.50 
TCGA-EA-A43B TCGA-EA-A5ZF TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A57G TCGA-HG-A2PA 
        1.81        14.96         1.22        23.84         1.32        25.41 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MU-A5YI 
       96.95        78.71        10.06         0.10         0.07         0.03 
TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-UC-A7PD 
        2.96         3.45        11.67 

$`6P GAIN WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       23.67        11.44        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-A1M8 
      177.04       173.29        82.85        19.86        67.46        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       57.73        53.16         0.46         2.43        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.18        73.45        83.05       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK 
        0.82        18.02        20.42       182.93       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 
       15.48         9.67        73.41        17.19        60.69         9.34 
TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       13.61        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QT 
      118.65        22.98        16.83        16.18         7.33        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       14.50         1.35         1.35        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       14.89         1.48        13.91         0.69        14.99        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.35         1.97         1.12 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       21.67        20.78        14.93         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       66.81       117.40        81.96        26.56        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AW 
       16.64        19.33        20.48        15.58         5.13         0.89 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
        0.82        13.87         5.42        29.72         0.07         4.34 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.72         5.85         3.39         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        6.25        19.59         3.88        93.99 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.03              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            96.95            182.93 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           17.850            12.935 
[1] "0.0 - 97.0 (17.9)"  "0.0 - 182.9 (12.9)"
[1] "hr=" "1.6"
D11V2, continuous
                   vv
clus                T1 T2+T3+T4
  6P GAIN MUTATED   16        9
  6P GAIN WILD-TYPE 81       30
D11V3, multiclass
          clus
vv         6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1                    16                81
  T2+T3+T4               9                30
[1] 2 2
[1] FALSE
D11V4, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   15  7
  6P GAIN WILD-TYPE 72 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     15    7
  6P GAIN WILD-TYPE   72   33
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              15                72
  1               7                33
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6P GAIN MUTATED   17  0  9
  6P GAIN WILD-TYPE 55  3 56
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              17                55
  M1               0                 3
  MX               9                56
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED               0                               29
  6P GAIN WILD-TYPE             2                              115
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6P GAIN MUTATED                                               1
  6P GAIN WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6P GAIN MUTATED                                     3
  6P GAIN WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6P GAIN MUTATED                                           0
  6P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6P GAIN MUTATED                                              2
  6P GAIN WILD-TYPE                                            2
D11V6, multiclass
                                               clus
vv                                              6P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           29
  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                                              6P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            115
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  2
[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"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     7  28
  6P GAIN WILD-TYPE  20 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      7   28
  6P GAIN WILD-TYPE   20  121
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                7                20
  YES              28               121
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  1     4
  6P GAIN WILD-TYPE                                6    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED                           4
  6P GAIN WILD-TYPE                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           0    26
  6P GAIN WILD-TYPE                                         1   104
D11V10, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   4                11
  BLACK OR AFRICAN AMERICAN                               4                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  26               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"
D11V11, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     1  26
  6P GAIN WILD-TYPE  10 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   26
  6P GAIN WILD-TYPE   10  101
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              26               101
[1] 2 2
[1] FALSE
D11V12, continuous
D11V13, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    7  8
  6P GAIN WILD-TYPE 41 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      7    8
  6P GAIN WILD-TYPE   41   11
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  TUMOR FREE               7                41
  WITH TUMOR               8                11
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  6P GAIN MUTATED         1      1       1            28       4
  6P GAIN WILD-TYPE       0      9       5           119       8
D11V14, multiclass
               clus
vv              6P GAIN MUTATED 6P GAIN WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      1                 9
  UKRAINE                     1                 5
  UNITED STATES              28               119
  VIETNAM                     4                 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                G1 G2 G3 G4 GX
  6P GAIN MUTATED    0 17 16  1  1
  6P GAIN WILD-TYPE 14 66 56  0  4
D11V15, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  G1               0                14
  G2              17                66
  G3              16                56
  G4               1                 0
  GX               1                 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"
D11V16, continuous
D11V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6P GAIN MUTATED                                             3
  6P GAIN WILD-TYPE                                          18
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  6P GAIN MUTATED                                        2
  6P GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  6P GAIN MUTATED                                                 0
  6P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6P GAIN MUTATED               10                  17
  6P GAIN WILD-TYPE             26                  66
D11V18, multiclass
                                                 clus
vv                                                6P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               10
  LIFELONG NON-SMOKER                                          17
                                                 clus
vv                                                6P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 26
  LIFELONG NON-SMOKER                                            66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  6P GAIN MUTATED             6        8             1        1
  6P GAIN WILD-TYPE          11       29            10        4
D11V20, multiclass
               clus
vv              6P GAIN MUTATED 6P GAIN WILD-TYPE
  COMBINATION                 6                11
  EXTERNAL                    8                29
  EXTERNAL BEAM               1                10
  INTERNAL                    1                 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"
D11V21, binary
                   cls
clus                0 1
  6P GAIN MUTATED   3 0
  6P GAIN WILD-TYPE 8 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    0
  6P GAIN WILD-TYPE    8    3
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  CGY               3                 8
  GY                0                 3
[1] 2 2
[1] FALSE
D11V22, continuous
D11V23, continuous
D11V24, continuous
D11V25, continuous
D11V26, continuous
D11V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  6P GAIN MUTATED                                     0
  6P GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  6P GAIN MUTATED                                     0                       1
  6P GAIN WILD-TYPE                                   6                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6P GAIN MUTATED                         0                       1
  6P GAIN WILD-TYPE                       1                       4
D11V28, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                21 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A50E 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EK-A2RN        TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-HM-A4S6        TCGA-IR-A3LI        TCGA-IR-A3LK 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-MU-A8JM 
"6P GAIN WILD-TYPE" 
                   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                                                3
  6P GAIN WILD-TYPE                                              7
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6P GAIN MUTATED                                                                                   9
  6P GAIN WILD-TYPE                                                                                45
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6P GAIN MUTATED                                                                                             17
  6P GAIN WILD-TYPE                                                                                           60
D11V29, multiclass
                                                                                              clus
vv                                                                                             6P 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)                          9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              17
                                                                                              clus
vv                                                                                             6P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               7
  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)                60
[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"
D11V30, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    9 11
  6P GAIN WILD-TYPE 45 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9   11
  6P GAIN WILD-TYPE   45   48
         clus
vv        6P GAIN MUTATED 6P GAIN WILD-TYPE
  ABSENT                9                45
  PRESENT              11                48
[1] 2 2
[1] FALSE
D11V31, continuous
D11V32, continuous
D11V33, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    5 15
  6P GAIN WILD-TYPE 30 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5   15
  6P GAIN WILD-TYPE   30   66
                                          clus
vv                                         6P GAIN MUTATED 6P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              15                66
[1] 2 2
[1] FALSE
D11V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  6P GAIN MUTATED       0                   20                   3
  6P GAIN WILD-TYPE     3                   93                   2
D11V35, multiclass
                      clus
vv                     6P GAIN MUTATED 6P GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              20                93
  SIMPLE HYSTERECTOMY                3                 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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6P GAIN MUTATED              0          10          7
  6P GAIN WILD-TYPE            8          30         33
D11V36, multiclass
              clus
vv             6P GAIN MUTATED 6P GAIN WILD-TYPE
  CURRENT USER               0                 8
  FORMER USER               10                30
  NEVER USED                 7                33
[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, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    9  4
  6P GAIN WILD-TYPE 64 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9    4
  6P GAIN WILD-TYPE   64   10
         clus
vv        6P GAIN MUTATED 6P GAIN WILD-TYPE
  ABSENT                9                64
  PRESENT               4                10
[1] 2 2
[1] FALSE
D11V39, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                 7 
       TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-HM-A3JK 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  6P GAIN MUTATED     0    1   2   10    3  1   1    3    1   2   1  0  1
  6P GAIN WILD-TYPE   2    0  20   41   18  2   5    3    7  11   1  1  6
D11V40, multiclass
      clus
vv     6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1A                0                 2
  T1A1               1                 0
  T1B                2                20
  T1B1              10                41
  T1B2               3                18
  T2                 1                 2
  T2A                1                 5
  T2A1               3                 3
  T2A2               1                 7
  T2B                2                11
  T3B                1                 1
  T4                 0                 1
  TX                 1                 6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V41, continuous

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    13   7
  6Q GAIN WILD-TYPE 124  25
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               20               149 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                7                25 
$`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-A3HD TCGA-C5-A3HF TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-DS-A7WI TCGA-EA-A1QS 
       52.01        17.85        85.55         2.73         8.28         0.76 
TCGA-EA-A439 TCGA-EA-A43B TCGA-HG-A2PA TCGA-IR-A3LH TCGA-JW-A69B TCGA-JW-A852 
       14.50         1.81        25.41        78.71        10.06         5.13 
TCGA-PN-A8MA TCGA-UC-A7PD 
        2.96        11.67 

$`6Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        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-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK 
       67.46        30.21        57.73        53.16         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-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HL 
       78.35       100.14        38.43         0.82        18.02        20.42 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
      182.93        25.35       101.82       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       73.41        17.19        60.69        94.95         9.34        13.61 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QT TCGA-EA-A3HQ 
       22.98        16.83        16.18         7.33        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
        1.35         1.35        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17         0.66         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.32         1.97         1.12        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       20.48        15.58         0.10         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        3.72         3.45         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        93.99 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.76              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            85.55            182.93 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            21.63             13.05 
[1] "0.8 - 85.5 (21.6)"  "0.0 - 182.9 (13.1)"
[1] "hr=" "2.1"
D12V2, continuous
                   vv
clus                T1 T2+T3+T4
  6Q GAIN MUTATED    8        7
  6Q GAIN WILD-TYPE 89       32
D12V3, multiclass
          clus
vv         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1                     8                89
  T2+T3+T4               7                32
[1] 2 2
[1] FALSE
D12V4, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    9  5
  6Q GAIN WILD-TYPE 78 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      9    5
  6Q GAIN WILD-TYPE   78   35
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               9                78
  1               5                35
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6Q GAIN MUTATED   11  0  4
  6Q GAIN WILD-TYPE 61  3 61
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              11                61
  M1               0                 3
  MX               4                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED               0                               17
  6Q GAIN WILD-TYPE             2                              127
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6Q GAIN MUTATED                                               0
  6Q GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6Q GAIN MUTATED                                     2
  6Q GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6Q GAIN MUTATED                                           0
  6Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6Q GAIN MUTATED                                              2
  6Q GAIN WILD-TYPE                                            2
D12V6, multiclass
                                               clus
vv                                              6Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           17
  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                                              6Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            127
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  2
[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"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     5  16
  6Q GAIN WILD-TYPE  22 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5   16
  6Q GAIN WILD-TYPE   22  133
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                5                22
  YES              16               133
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  1     1
  6Q GAIN WILD-TYPE                                6    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED                           2
  6Q GAIN WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           0    17
  6Q GAIN WILD-TYPE                                         1   113
D12V10, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   1                14
  BLACK OR AFRICAN AMERICAN                               2                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  17               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"
D12V11, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  14
  6Q GAIN WILD-TYPE   9 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   14
  6Q GAIN WILD-TYPE    9  113
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              14               113
[1] 2 2
[1] FALSE
D12V12, continuous
D12V13, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    5  6
  6Q GAIN WILD-TYPE 43 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5    6
  6Q GAIN WILD-TYPE   43   13
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  TUMOR FREE               5                43
  WITH TUMOR               6                13
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  6Q GAIN MUTATED         1      1       1            17       1
  6Q GAIN WILD-TYPE       0      9       5           130      11
D12V14, multiclass
               clus
vv              6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      1                 9
  UKRAINE                     1                 5
  UNITED STATES              17               130
  VIETNAM                     1                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"
                   vv
clus                G1 G2 G3 G4 GX
  6Q GAIN MUTATED    0 12  7  1  1
  6Q GAIN WILD-TYPE 14 71 65  0  4
D12V15, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  G1               0                14
  G2              12                71
  G3               7                65
  G4               1                 0
  GX               1                 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"
D12V16, continuous
D12V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6Q GAIN MUTATED                                             2
  6Q GAIN WILD-TYPE                                          19
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  6Q GAIN MUTATED                                        1
  6Q GAIN WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  6Q GAIN MUTATED                                                 0
  6Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6Q GAIN MUTATED                8                   8
  6Q GAIN WILD-TYPE             28                  75
D12V18, multiclass
                                                 clus
vv                                                6Q 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                                                8
  LIFELONG NON-SMOKER                                           8
                                                 clus
vv                                                6Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 28
  LIFELONG NON-SMOKER                                            75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  6Q GAIN MUTATED             4        5             1        1
  6Q GAIN WILD-TYPE          13       32            10        4
D12V20, multiclass
               clus
vv              6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COMBINATION                 4                13
  EXTERNAL                    5                32
  EXTERNAL BEAM               1                10
  INTERNAL                    1                 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"
D12V21, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  0
  6Q GAIN WILD-TYPE 10  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    0
  6Q GAIN WILD-TYPE   10    3
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CGY               1                10
  GY                0                 3
[1] 2 2
[1] FALSE
D12V22, continuous
D12V23, continuous
D12V24, continuous
D12V25, continuous
D12V26, continuous
D12V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  6Q GAIN MUTATED                                     0
  6Q GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  6Q GAIN MUTATED                                     0                       1
  6Q GAIN WILD-TYPE                                   6                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6Q GAIN MUTATED                         0                       1
  6Q GAIN WILD-TYPE                       1                       4
D12V28, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                21 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A50E 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EK-A2RN        TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-HM-A4S6        TCGA-IR-A3LI        TCGA-IR-A3LK 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-MU-A8JM 
"6Q GAIN WILD-TYPE" 
                   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                                                1
  6Q GAIN WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6Q GAIN MUTATED                                                                                   4
  6Q GAIN WILD-TYPE                                                                                50
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6Q GAIN MUTATED                                                                                             13
  6Q GAIN WILD-TYPE                                                                                           64
D12V29, multiclass
                                                                                              clus
vv                                                                                             6Q 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)                          4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              13
                                                                                              clus
vv                                                                                             6Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           50
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                64
[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"
D12V30, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    4  7
  6Q GAIN WILD-TYPE 50 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4    7
  6Q GAIN WILD-TYPE   50   52
         clus
vv        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ABSENT                4                50
  PRESENT               7                52
[1] 2 2
[1] FALSE
D12V31, continuous
D12V32, continuous
D12V33, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    4  8
  6Q GAIN WILD-TYPE 31 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4    8
  6Q GAIN WILD-TYPE   31   73
                                          clus
vv                                         6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   4                31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               8                73
[1] 2 2
[1] FALSE
D12V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  6Q GAIN MUTATED       0                   12                   0
  6Q GAIN WILD-TYPE     3                  101                   5
D12V35, multiclass
                      clus
vv                     6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              12               101
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6Q GAIN MUTATED              0           6          5
  6Q GAIN WILD-TYPE            8          34         35
D12V36, multiclass
              clus
vv             6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  CURRENT USER               0                 8
  FORMER USER                6                34
  NEVER USED                 5                35
[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, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    5  2
  6Q GAIN WILD-TYPE 68 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      5    2
  6Q GAIN WILD-TYPE   68   12
         clus
vv        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ABSENT                5                68
  PRESENT               2                12
[1] 2 2
[1] FALSE
D12V39, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                 7 
       TCGA-C5-A1BN        TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-EK-A2RO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-MU-A51Y        TCGA-MU-A8JM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  6Q GAIN MUTATED     0    0   2    4    2  0   1    2    1   2   1  0  0
  6Q GAIN WILD-TYPE   2    1  20   47   19  3   5    4    7  11   1  1  7
D12V40, multiclass
      clus
vv     6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                2                20
  T1B1               4                47
  T1B2               2                19
  T2                 0                 3
  T2A                1                 5
  T2A1               2                 4
  T2A2               1                 7
  T2B                2                11
  T3B                1                 1
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V41, continuous

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    18   5
  7P GAIN WILD-TYPE 119  27
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               23               146 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                27 
$`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        25.35 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-EA-A50E TCGA-EK-A2GZ 
       73.41        17.19        60.69        94.95         0.26        12.59 
TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-FU-A23L TCGA-FU-A40J 
        0.53         0.07         0.36         1.18        23.84         1.35 
TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-JW-A69B TCGA-Q1-A6DT TCGA-R2-A69V 
       36.36        19.33        10.06         3.39        19.59 

$`7P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16        38.99        35.61         0.46        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       44.22        73.45        83.05        38.43         0.82        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       182.93       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       15.48         9.67        85.55         9.34        13.61         2.73 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
       12.36         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
        1.18        14.50         1.35         1.35        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.66        12.82        14.89         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.99        14.96        13.58        13.48        45.96         6.64 
TCGA-EK-A2R7 TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.59         4.04         0.03        23.70         2.24         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG 
        6.94        14.70         4.47         6.12         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         3.52         1.32         1.97         1.12        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         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU 
       14.43        16.64        20.48        15.58         5.13         0.10 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.89         0.07         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         2.96         3.72         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 
        5.85         3.72         5.75         4.80         6.25         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           173.29            182.93 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           19.330            13.265 
[1] "0.1 - 173.3 (19.3)" "0.0 - 182.9 (13.3)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                T1 T2+T3+T4
  7P GAIN MUTATED    9        5
  7P GAIN WILD-TYPE 88       34
D13V3, multiclass
          clus
vv         7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                     9                88
  T2+T3+T4               5                34
[1] 2 2
[1] FALSE
D13V4, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    9  3
  7P GAIN WILD-TYPE 78 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9    3
  7P GAIN WILD-TYPE   78   37
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0               9                78
  1               3                37
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED    7  0  8
  7P GAIN WILD-TYPE 65  3 57
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0               7                65
  M1               0                 3
  MX               8                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED               0                               21
  7P GAIN WILD-TYPE             2                              123
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7P GAIN MUTATED                                               0
  7P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7P GAIN MUTATED                                     2
  7P GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7P GAIN MUTATED                                           0
  7P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7P GAIN MUTATED                                              0
  7P GAIN WILD-TYPE                                            4
D13V6, multiclass
                                               clus
vv                                              7P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           21
  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                                              7P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     4  19
  7P GAIN WILD-TYPE  23 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4   19
  7P GAIN WILD-TYPE   23  130
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                4                23
  YES              19               130
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     1
  7P GAIN WILD-TYPE                                6    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED                           3
  7P GAIN WILD-TYPE                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           0    18
  7P GAIN WILD-TYPE                                         1   112
D13V10, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   1                14
  BLACK OR AFRICAN AMERICAN                               3                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  18               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"
D13V11, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     2  17
  7P GAIN WILD-TYPE   9 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   17
  7P GAIN WILD-TYPE    9  110
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              17               110
[1] 2 2
[1] FALSE
D13V12, continuous
D13V13, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5  4
  7P GAIN WILD-TYPE 43 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5    4
  7P GAIN WILD-TYPE   43   15
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  TUMOR FREE               5                43
  WITH TUMOR               4                15
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  7P GAIN MUTATED         0      0       0            22       1
  7P GAIN WILD-TYPE       1     10       6           125      11
D13V14, multiclass
               clus
vv              7P GAIN MUTATED 7P GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 6
  UNITED STATES              22               125
  VIETNAM                     1                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"
                   vv
clus                G1 G2 G3 G4 GX
  7P GAIN MUTATED    0  9 12  0  2
  7P GAIN WILD-TYPE 14 74 60  1  3
D13V15, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  G1               0                14
  G2               9                74
  G3              12                60
  G4               0                 1
  GX               2                 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"
D13V16, continuous
[1] "Remove cluster labels:" "7P GAIN MUTATED"       
clus
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                23 
       TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BQ        TCGA-C5-A1ME 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A2M2        TCGA-C5-A3HD 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-C5-A7CM        TCGA-DS-A3LQ        TCGA-EX-A69M        TCGA-FU-A2QG 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-HM-A3JK        TCGA-HM-A4S6 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-MU-A5YI 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
D13V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7P GAIN MUTATED                                             1
  7P GAIN WILD-TYPE                                          20
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  7P GAIN MUTATED                                        1
  7P GAIN WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  7P GAIN MUTATED                                                 0
  7P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7P GAIN MUTATED                4                  12
  7P GAIN WILD-TYPE             32                  71
D13V18, multiclass
                                                 clus
vv                                                7P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                4
  LIFELONG NON-SMOKER                                          12
                                                 clus
vv                                                7P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 32
  LIFELONG NON-SMOKER                                            71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  7P GAIN MUTATED             3        4             1        2
  7P GAIN WILD-TYPE          14       33            10        3
D13V20, multiclass
               clus
vv              7P GAIN MUTATED 7P GAIN WILD-TYPE
  COMBINATION                 3                14
  EXTERNAL                    4                33
  EXTERNAL BEAM               1                10
  INTERNAL                    2                 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"
D13V21, binary
                   cls
clus                0 1
  7P GAIN MUTATED   2 1
  7P GAIN WILD-TYPE 9 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2    1
  7P GAIN WILD-TYPE    9    2
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  CGY               2                 9
  GY                1                 2
[1] 2 2
[1] FALSE
D13V22, continuous
D13V23, continuous
D13V24, continuous
D13V25, continuous
D13V26, continuous
D13V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  7P GAIN MUTATED                                     0
  7P GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  7P GAIN MUTATED                                     0                       0
  7P GAIN WILD-TYPE                                   6                       9
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7P GAIN MUTATED                         1                       0
  7P GAIN WILD-TYPE                       0                       5
D13V28, multiclass
[1] "Remove cluster labels:" "7P GAIN MUTATED"       
clus
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                1                22 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EK-A2RN 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-UC-A7PD 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
                   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                                                1
  7P GAIN WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7P GAIN MUTATED                                                                                   9
  7P GAIN WILD-TYPE                                                                                45
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7P GAIN MUTATED                                                                                              7
  7P GAIN WILD-TYPE                                                                                           70
D13V29, multiclass
                                                                                              clus
vv                                                                                             7P 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)               7
                                                                                              clus
vv                                                                                             7P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                70
[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"
D13V30, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    3  7
  7P GAIN WILD-TYPE 51 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3    7
  7P GAIN WILD-TYPE   51   52
         clus
vv        7P GAIN MUTATED 7P GAIN WILD-TYPE
  ABSENT                3                51
  PRESENT               7                52
[1] 2 2
[1] FALSE
D13V31, continuous
D13V32, continuous
D13V33, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5 10
  7P GAIN WILD-TYPE 30 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5   10
  7P GAIN WILD-TYPE   30   71
                                          clus
vv                                         7P GAIN MUTATED 7P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              10                71
[1] 2 2
[1] FALSE
D13V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  7P GAIN MUTATED       0                    9                   0
  7P GAIN WILD-TYPE     3                  104                   5
D13V35, multiclass
                      clus
vv                     7P GAIN MUTATED 7P GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY               9               104
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7P GAIN MUTATED              1           3          3
  7P GAIN WILD-TYPE            7          37         37
D13V36, multiclass
              clus
vv             7P GAIN MUTATED 7P GAIN WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                3                37
  NEVER USED                 3                37
[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
D13V38, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    7  2
  7P GAIN WILD-TYPE 66 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      7    2
  7P GAIN WILD-TYPE   66   12
         clus
vv        7P GAIN MUTATED 7P GAIN WILD-TYPE
  ABSENT                7                66
  PRESENT               2                12
[1] 2 2
[1] FALSE
D13V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  7P GAIN MUTATED     0    0   4    3    2  0   0    2    1   1   0  1  1
  7P GAIN WILD-TYPE   2    1  18   48   19  3   6    4    7  12   2  0  6
D13V40, multiclass
      clus
vv     7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                4                18
  T1B1               3                48
  T1B2               2                19
  T2                 0                 3
  T2A                0                 6
  T2A1               2                 4
  T2A2               1                 7
  T2B                1                12
  T3B                0                 2
  T4                 1                 0
  TX                 1                 6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V41, continuous

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    18   4
  7Q GAIN WILD-TYPE 119  28
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22               147 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                28 
$`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-A7CH TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-DR-A0ZL 
       25.35        73.41        17.19        60.69        94.95        87.75 
TCGA-DS-A3LQ TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RJ TCGA-FU-A23L 
       22.98        12.59         0.53         0.07         1.18        23.84 
TCGA-FU-A3NI TCGA-IR-A3LL TCGA-JW-A5VK TCGA-JW-A69B 
        1.45        36.36        20.48        10.06 

$`7Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       177.04        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       38.99        35.61         0.46        40.93         3.58        44.22 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       73.45        83.05        38.43         0.82        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       182.93       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM 
        9.67        85.55         9.34        13.61         2.73        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       117.99       118.65        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        7.33         8.28         0.76        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35        14.50         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RC 
       13.58        13.48        45.96         6.64         0.59         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        0.03         0.36        23.70         2.24         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         4.47         6.12         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.66         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.35         1.32         1.97         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         4.11       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        26.56        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       16.64        19.33        15.58         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           173.29            182.93 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           24.595            12.660 
[1] "0.1 - 173.3 (24.6)" "0.0 - 182.9 (12.7)"
[1] "hr=" "1.7"
D14V2, continuous
                   vv
clus                T1 T2+T3+T4
  7Q GAIN MUTATED   12        2
  7Q GAIN WILD-TYPE 85       37
D14V3, multiclass
          clus
vv         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                    12                85
  T2+T3+T4               2                37
[1] 2 2
[1] FALSE
D14V4, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    9  3
  7Q GAIN WILD-TYPE 78 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      9    3
  7Q GAIN WILD-TYPE   78   37
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0               9                78
  1               3                37
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED    7  0  7
  7Q GAIN WILD-TYPE 65  3 58
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0               7                65
  M1               0                 3
  MX               7                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED               0                               21
  7Q GAIN WILD-TYPE             2                              123
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7Q GAIN MUTATED                                               0
  7Q GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7Q GAIN MUTATED                                     1
  7Q GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7Q GAIN MUTATED                                           0
  7Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7Q GAIN MUTATED                                              0
  7Q GAIN WILD-TYPE                                            4
D14V6, multiclass
                                               clus
vv                                              7Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           21
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              7Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     6  16
  7Q GAIN WILD-TYPE  21 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6   16
  7Q GAIN WILD-TYPE   21  133
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                6                21
  YES              16               133
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     1
  7Q GAIN WILD-TYPE                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED                           4
  7Q GAIN WILD-TYPE                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           0    16
  7Q GAIN WILD-TYPE                                         1   114
D14V10, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   1                14
  BLACK OR AFRICAN AMERICAN                               4                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  16               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"
D14V11, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     1  16
  7Q GAIN WILD-TYPE  10 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   16
  7Q GAIN WILD-TYPE   10  111
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              16               111
[1] 2 2
[1] FALSE
D14V12, continuous
D14V13, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7  2
  7Q GAIN WILD-TYPE 41 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7    2
  7Q GAIN WILD-TYPE   41   17
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  TUMOR FREE               7                41
  WITH TUMOR               2                17
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  7Q GAIN MUTATED         0      0       0            22       0
  7Q GAIN WILD-TYPE       1     10       6           125      12
D14V14, multiclass
               clus
vv              7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 6
  UNITED STATES              22               125
  VIETNAM                     0                12
[1] 5 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                G1 G2 G3 G4 GX
  7Q GAIN MUTATED    0  9 12  0  1
  7Q GAIN WILD-TYPE 14 74 60  1  4
D14V15, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  G1               0                14
  G2               9                74
  G3              12                60
  G4               0                 1
  GX               1                 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"
D14V16, continuous
D14V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7Q GAIN MUTATED                                             2
  7Q GAIN WILD-TYPE                                          19
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  7Q GAIN MUTATED                                        3
  7Q GAIN WILD-TYPE                                      5
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  7Q GAIN MUTATED                                                 0
  7Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7Q GAIN MUTATED                5                   8
  7Q GAIN WILD-TYPE             31                  75
D14V18, multiclass
                                                 clus
vv                                                7Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                5
  LIFELONG NON-SMOKER                                           8
                                                 clus
vv                                                7Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 31
  LIFELONG NON-SMOKER                                            75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  7Q GAIN MUTATED             4        3             2        2
  7Q GAIN WILD-TYPE          13       34             9        3
D14V20, multiclass
               clus
vv              7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COMBINATION                 4                13
  EXTERNAL                    3                34
  EXTERNAL BEAM               2                 9
  INTERNAL                    2                 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"
D14V21, binary
                   cls
clus                0 1
  7Q GAIN MUTATED   2 0
  7Q GAIN WILD-TYPE 9 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2    0
  7Q GAIN WILD-TYPE    9    3
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CGY               2                 9
  GY                0                 3
[1] 2 2
[1] FALSE
D14V22, continuous
D14V23, continuous
D14V24, continuous
D14V25, continuous
D14V26, continuous
D14V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  7Q GAIN MUTATED                                     0
  7Q GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  7Q GAIN MUTATED                                     0                       1
  7Q GAIN WILD-TYPE                                   6                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7Q GAIN MUTATED                         0                       0
  7Q GAIN WILD-TYPE                       1                       5
D14V28, multiclass
[1] "Remove cluster labels:" "7Q GAIN MUTATED"       
clus
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                22 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-EA-A50E        TCGA-EK-A2RN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-UC-A7PD 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
                   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                                                0
  7Q GAIN WILD-TYPE                                             10
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7Q GAIN MUTATED                                                                                   8
  7Q GAIN WILD-TYPE                                                                                46
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7Q GAIN MUTATED                                                                                              8
  7Q GAIN WILD-TYPE                                                                                           69
D14V29, multiclass
                                                                                              clus
vv                                                                                             7Q 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)                          8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               8
                                                                                              clus
vv                                                                                             7Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           46
  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"
D14V30, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5  5
  7Q GAIN WILD-TYPE 49 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5    5
  7Q GAIN WILD-TYPE   49   54
         clus
vv        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ABSENT                5                49
  PRESENT               5                54
[1] 2 2
[1] FALSE
D14V31, continuous
D14V32, continuous
D14V33, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    6  9
  7Q GAIN WILD-TYPE 29 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6    9
  7Q GAIN WILD-TYPE   29   72
                                          clus
vv                                         7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               9                72
[1] 2 2
[1] FALSE
D14V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  7Q GAIN MUTATED       0                   10                   0
  7Q GAIN WILD-TYPE     3                  103                   5
D14V35, multiclass
                      clus
vv                     7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              10               103
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7Q GAIN MUTATED              1           4          4
  7Q GAIN WILD-TYPE            7          36         36
D14V36, multiclass
              clus
vv             7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                4                36
  NEVER USED                 4                36
[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
D14V38, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    6  1
  7Q GAIN WILD-TYPE 67 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6    1
  7Q GAIN WILD-TYPE   67   13
         clus
vv        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ABSENT                6                67
  PRESENT               1                13
[1] 2 2
[1] FALSE
D14V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  7Q GAIN MUTATED     0    0   3    5    4  0   0    1    0   0   1  0  0
  7Q GAIN WILD-TYPE   2    1  19   46   17  3   6    5    8  13   1  1  7
D14V40, multiclass
      clus
vv     7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                3                19
  T1B1               5                46
  T1B2               4                17
  T2                 0                 3
  T2A                0                 6
  T2A1               1                 5
  T2A2               0                 8
  T2B                0                13
  T3B                1                 1
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V41, continuous

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    21   6
  8P GAIN WILD-TYPE 116  26
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               27               142 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                26 
$`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       182.93        25.35        60.69 
TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E 
       22.98         1.74        14.50         1.35        12.82         0.26 
TCGA-EA-A5O9 TCGA-EK-A2RN TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A57G TCGA-IR-A3LL 
       13.91         0.10         1.45         3.52         1.32        36.36 
TCGA-MY-A5BF TCGA-Q1-A5R2 TCGA-Q1-A6DW 
        4.34         3.45         5.75 

$`8P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 
      144.16       177.04       173.29         5.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       30.21        35.01        57.73         0.46         2.43        40.93 
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-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ 
       38.43         0.82        52.01        17.85        20.42       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48         9.67        73.41        17.19        85.55 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       94.95         9.34        13.61         2.73        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       117.99       118.65        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
        7.33         8.28         0.76        12.36         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B 
        0.62        13.05         1.18         1.35        14.50         1.81 
TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       12.66        14.89         1.48         0.69        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.58        13.48        12.59        45.96         6.64         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.59         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       23.70         2.24         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17         0.66         1.02 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 
        1.58         1.48         0.82         1.35         1.97         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       26.56        14.43        16.64        19.33        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       10.06         5.13         0.10         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA 
       13.87         0.03         5.42        29.72         0.07         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A73P TCGA-Q1-A73R 
        3.72         5.85         3.39         3.72         4.80         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.10              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           182.93            177.04 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           14.500            13.265 
[1] "0.1 - 182.9 (14.5)" "0.0 - 177.0 (13.3)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                T1 T2+T3+T4
  8P GAIN MUTATED   15        6
  8P GAIN WILD-TYPE 82       33
D15V3, multiclass
          clus
vv         8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                    15                82
  T2+T3+T4               6                33
[1] 2 2
[1] FALSE
D15V4, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   14  7
  8P GAIN WILD-TYPE 73 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     14    7
  8P GAIN WILD-TYPE   73   33
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              14                73
  1               7                33
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED   12  0 11
  8P GAIN WILD-TYPE 60  3 54
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              12                60
  M1               0                 3
  MX              11                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED               0                               26
  8P GAIN WILD-TYPE             2                              118
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8P GAIN MUTATED                                               0
  8P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8P GAIN MUTATED                                     2
  8P GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8P GAIN MUTATED                                           0
  8P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8P GAIN MUTATED                                              0
  8P GAIN WILD-TYPE                                            4
D15V6, multiclass
                                               clus
vv                                              8P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           26
  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                                              8P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            118
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     5  23
  8P GAIN WILD-TYPE  22 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5   23
  8P GAIN WILD-TYPE   22  126
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                5                22
  YES              23               126
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     1
  8P GAIN WILD-TYPE                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED                           2
  8P GAIN WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           0    24
  8P GAIN WILD-TYPE                                         1   106
D15V10, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   1                14
  BLACK OR AFRICAN AMERICAN                               2                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  24               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"
D15V11, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0  23
  8P GAIN WILD-TYPE  11 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   23
  8P GAIN WILD-TYPE   11  104
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              23               104
[1] 2 2
[1] FALSE
D15V12, continuous
D15V13, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    9  4
  8P GAIN WILD-TYPE 39 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9    4
  8P GAIN WILD-TYPE   39   15
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  TUMOR FREE               9                39
  WITH TUMOR               4                15
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  8P GAIN MUTATED         0      2       3            22       1
  8P GAIN WILD-TYPE       1      8       3           125      11
D15V14, multiclass
               clus
vv              8P GAIN MUTATED 8P GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      2                 8
  UKRAINE                     3                 3
  UNITED STATES              22               125
  VIETNAM                     1                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"
                   vv
clus                G1 G2 G3 G4 GX
  8P GAIN MUTATED    2 16  9  0  1
  8P GAIN WILD-TYPE 12 67 63  1  4
D15V15, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  G1               2                12
  G2              16                67
  G3               9                63
  G4               0                 1
  GX               1                 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"
D15V16, continuous
D15V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8P GAIN MUTATED                                             4
  8P GAIN WILD-TYPE                                          17
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  8P GAIN MUTATED                                        2
  8P GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  8P GAIN MUTATED                                                 0
  8P GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8P GAIN MUTATED                4                  16
  8P GAIN WILD-TYPE             32                  67
D15V18, multiclass
                                                 clus
vv                                                8P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                4
  LIFELONG NON-SMOKER                                          16
                                                 clus
vv                                                8P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 32
  LIFELONG NON-SMOKER                                            67
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  8P GAIN MUTATED             5        7             1        1
  8P GAIN WILD-TYPE          12       30            10        4
D15V20, multiclass
               clus
vv              8P GAIN MUTATED 8P GAIN WILD-TYPE
  COMBINATION                 5                12
  EXTERNAL                    7                30
  EXTERNAL BEAM               1                10
  INTERNAL                    1                 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"
D15V21, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    0  0
  8P GAIN WILD-TYPE 11  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0    0
  8P GAIN WILD-TYPE   11    3
D15V22, continuous
D15V23, continuous
D15V24, continuous
D15V25, continuous
D15V26, continuous
D15V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  8P GAIN MUTATED                                     0
  8P GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  8P GAIN MUTATED                                     0                       2
  8P GAIN WILD-TYPE                                   6                       7
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8P GAIN MUTATED                         1                       1
  8P GAIN WILD-TYPE                       0                       4
D15V28, multiclass
                                     clus
vv                                    8P GAIN MUTATED 8P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           2                 7
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           1                 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)
  8P GAIN MUTATED                                               1
  8P GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  8P GAIN MUTATED                                                1
  8P GAIN WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8P GAIN MUTATED                                                                                  10
  8P GAIN WILD-TYPE                                                                                44
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8P GAIN MUTATED                                                                                             12
  8P GAIN WILD-TYPE                                                                                           65
D15V29, multiclass
                                                                                              clus
vv                                                                                             8P GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  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)              12
                                                                                              clus
vv                                                                                             8P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                65
[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"
D15V30, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    9 10
  8P GAIN WILD-TYPE 45 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   10
  8P GAIN WILD-TYPE   45   49
         clus
vv        8P GAIN MUTATED 8P GAIN WILD-TYPE
  ABSENT                9                45
  PRESENT              10                49
[1] 2 2
[1] FALSE
D15V31, continuous
D15V32, continuous
D15V33, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    9 12
  8P GAIN WILD-TYPE 26 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   12
  8P GAIN WILD-TYPE   26   69
                                          clus
vv                                         8P GAIN MUTATED 8P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   9                26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              12                69
[1] 2 2
[1] FALSE
D15V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  8P GAIN MUTATED       1                   19                   1
  8P GAIN WILD-TYPE     2                   94                   4
D15V35, multiclass
                      clus
vv                     8P GAIN MUTATED 8P GAIN WILD-TYPE
  OTHER                              1                 2
  RADICAL HYSTERECTOMY              19                94
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8P GAIN MUTATED              0           8          4
  8P GAIN WILD-TYPE            8          32         36
D15V36, multiclass
              clus
vv             8P GAIN MUTATED 8P GAIN WILD-TYPE
  CURRENT USER               0                 8
  FORMER USER                8                32
  NEVER USED                 4                36
[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, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   11  2
  8P GAIN WILD-TYPE 62 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     11    2
  8P GAIN WILD-TYPE   62   12
         clus
vv        8P GAIN MUTATED 8P GAIN WILD-TYPE
  ABSENT               11                62
  PRESENT               2                12
[1] 2 2
[1] FALSE
D15V39, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                 7 
       TCGA-C5-A1BN        TCGA-C5-A1MN        TCGA-EK-A2RO        TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  8P GAIN MUTATED     0    0   3    6    6  1   1    0    1   1   1  1  2
  8P GAIN WILD-TYPE   2    1  19   45   15  2   5    6    7  12   1  0  5
D15V40, multiclass
      clus
vv     8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                3                19
  T1B1               6                45
  T1B2               6                15
  T2                 1                 2
  T2A                1                 5
  T2A1               0                 6
  T2A2               1                 7
  T2B                1                12
  T3B                1                 1
  T4                 1                 0
  TX                 2                 5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V41, continuous

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    37   8
  8Q GAIN WILD-TYPE 100  24
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               45               124 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                24 
$`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       182.93 
TCGA-C5-A7CH TCGA-C5-A7UH TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3Y4 
       25.35        60.69       117.99        22.98         1.74        14.50 
TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EK-A2H0 
        1.35        12.82         0.26        14.89        13.91        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
        6.64         0.53         0.10         0.07         0.10         0.03 
TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3YQ TCGA-FU-A57G TCGA-IR-A3LL 
        6.12        23.84         1.45         3.52         1.32        36.36 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-MU-A5YI TCGA-MY-A5BF TCGA-Q1-A5R2 
        5.13         0.10         0.07         0.03         4.34         3.45 
TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-RA-A741 
        3.39         5.75         3.88 

$`8Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M7 
      144.16       177.04       173.29         5.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       30.21        35.01        57.73         0.46         2.43        40.93 
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         0.82 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       52.01        17.85        20.42       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
        9.67        73.41        17.19        85.55        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       13.61         2.73        87.75        58.88        36.76         2.66 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
      118.65        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       12.36         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A5FO TCGA-EA-A5ZD 
        1.35        14.50         1.81        12.66         1.48         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2R7 
       14.99        14.96        13.58        13.48        12.59         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        2.24         0.10        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        4.47         1.22         0.92         2.17         0.66         1.02 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A5XV TCGA-FU-A770 
        1.58         1.48         0.82         1.35         1.97         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       26.56        14.43        16.64        19.33        20.48        15.58 
TCGA-JW-A69B TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD 
       10.06         0.89         0.82        13.87         5.42        29.72 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A73P 
        0.07         2.96         3.72         5.85         3.72         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        19.59        11.67        93.99 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.03              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           182.93            177.04 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             6.64             13.74 
[1] "0.0 - 182.9 (6.6)"  "0.0 - 177.0 (13.7)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                T1 T2+T3+T4
  8Q GAIN MUTATED   24        9
  8Q GAIN WILD-TYPE 73       30
D16V3, multiclass
          clus
vv         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                    24                73
  T2+T3+T4               9                30
[1] 2 2
[1] FALSE
D16V4, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   21 11
  8Q GAIN WILD-TYPE 66 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     21   11
  8Q GAIN WILD-TYPE   66   29
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              21                66
  1              11                29
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED   17  0 18
  8Q GAIN WILD-TYPE 55  3 47
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              17                55
  M1               0                 3
  MX              18                47
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED               0                               44
  8Q GAIN WILD-TYPE             2                              100
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8Q GAIN MUTATED                                               0
  8Q GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8Q GAIN MUTATED                                     2
  8Q GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8Q GAIN MUTATED                                           1
  8Q GAIN WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8Q GAIN MUTATED                                              0
  8Q GAIN WILD-TYPE                                            4
D16V6, multiclass
                                               clus
vv                                              8Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           44
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              8Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            100
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     5  42
  8Q GAIN WILD-TYPE  22 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5   42
  8Q GAIN WILD-TYPE   22  107
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                5                22
  YES              42               107
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  1     3
  8Q GAIN WILD-TYPE                                6    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED                           5
  8Q GAIN WILD-TYPE                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           1    36
  8Q GAIN WILD-TYPE                                         0    94
D16V10, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   3                12
  BLACK OR AFRICAN AMERICAN                               5                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  36                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"
D16V11, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    2 34
  8Q GAIN WILD-TYPE  9 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2   34
  8Q GAIN WILD-TYPE    9   93
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              34                93
[1] 2 2
[1] FALSE
D16V12, continuous
D16V13, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   14  5
  8Q GAIN WILD-TYPE 34 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     14    5
  8Q GAIN WILD-TYPE   34   14
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  TUMOR FREE              14                34
  WITH TUMOR               5                14
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  8Q GAIN MUTATED         0      3       3            38       3
  8Q GAIN WILD-TYPE       1      7       3           109       9
D16V14, multiclass
               clus
vv              8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      3                 7
  UKRAINE                     3                 3
  UNITED STATES              38               109
  VIETNAM                     3                 9
[1] 5 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                G1 G2 G3 G4 GX
  8Q GAIN MUTATED    3 19 22  0  3
  8Q GAIN WILD-TYPE 11 64 50  1  2
D16V15, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  G1               3                11
  G2              19                64
  G3              22                50
  G4               0                 1
  GX               3                 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"
D16V16, continuous
D16V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8Q GAIN MUTATED                                             6
  8Q GAIN WILD-TYPE                                          15
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  8Q GAIN MUTATED                                        3
  8Q GAIN WILD-TYPE                                      5
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  8Q GAIN MUTATED                                                 0
  8Q GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8Q GAIN MUTATED                7                  22
  8Q GAIN WILD-TYPE             29                  61
D16V18, multiclass
                                                 clus
vv                                                8Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                7
  LIFELONG NON-SMOKER                                          22
                                                 clus
vv                                                8Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 29
  LIFELONG NON-SMOKER                                            61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  8Q GAIN MUTATED             5        9             1        2
  8Q GAIN WILD-TYPE          12       28            10        3
D16V20, multiclass
               clus
vv              8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COMBINATION                 5                12
  EXTERNAL                    9                28
  EXTERNAL BEAM               1                10
  INTERNAL                    2                 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"
D16V21, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    1  1
  8Q GAIN WILD-TYPE 10  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1    1
  8Q GAIN WILD-TYPE   10    2
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CGY               1                10
  GY                1                 2
[1] 2 2
[1] FALSE
D16V22, continuous
D16V23, continuous
D16V24, continuous
D16V25, continuous
D16V26, continuous
D16V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  8Q GAIN MUTATED                                     1
  8Q GAIN WILD-TYPE                                   1
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  8Q GAIN MUTATED                                     0                       3
  8Q GAIN WILD-TYPE                                   6                       6
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8Q GAIN MUTATED                         1                       1
  8Q GAIN WILD-TYPE                       0                       4
D16V28, multiclass
                                     clus
vv                                    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           3                 6
  POSITIVE BLADDER MARGIN                           1                 0
  POSITIVE VAGINAL MARGIN                           1                 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)
  8Q GAIN MUTATED                                               1
  8Q GAIN WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  8Q GAIN MUTATED                                                2
  8Q GAIN WILD-TYPE                                              8
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8Q GAIN MUTATED                                                                                  19
  8Q GAIN WILD-TYPE                                                                                35
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8Q GAIN MUTATED                                                                                             18
  8Q GAIN WILD-TYPE                                                                                           59
D16V29, multiclass
                                                                                              clus
vv                                                                                             8Q 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)                         19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              18
                                                                                              clus
vv                                                                                             8Q GAIN WILD-TYPE
  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)                           35
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                59
[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"
D16V30, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   14 12
  8Q GAIN WILD-TYPE 40 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     14   12
  8Q GAIN WILD-TYPE   40   47
         clus
vv        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ABSENT               14                40
  PRESENT              12                47
[1] 2 2
[1] FALSE
D16V31, continuous
D16V32, continuous
D16V33, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   12 22
  8Q GAIN WILD-TYPE 23 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     12   22
  8Q GAIN WILD-TYPE   23   59
                                          clus
vv                                         8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  12                23
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              22                59
[1] 2 2
[1] FALSE
D16V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  8Q GAIN MUTATED       1                   27                   3
  8Q GAIN WILD-TYPE     2                   86                   2
D16V35, multiclass
                      clus
vv                     8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  OTHER                              1                 2
  RADICAL HYSTERECTOMY              27                86
  SIMPLE HYSTERECTOMY                3                 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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8Q GAIN MUTATED              0           9          7
  8Q GAIN WILD-TYPE            8          31         33
D16V36, multiclass
              clus
vv             8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CURRENT USER               0                 8
  FORMER USER                9                31
  NEVER USED                 7                33
[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, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   16  3
  8Q GAIN WILD-TYPE 57 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     16    3
  8Q GAIN WILD-TYPE   57   11
         clus
vv        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ABSENT               16                57
  PRESENT               3                11
[1] 2 2
[1] FALSE
D16V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  8Q GAIN MUTATED     0    1   4   12    7  2   1    1    1   2   1  1  4
  8Q GAIN WILD-TYPE   2    0  18   39   14  1   5    5    7  11   1  0  3
D16V40, multiclass
      clus
vv     8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1A                0                 2
  T1A1               1                 0
  T1B                4                18
  T1B1              12                39
  T1B2               7                14
  T2                 2                 1
  T2A                1                 5
  T2A1               1                 5
  T2A2               1                 7
  T2B                2                11
  T3B                1                 1
  T4                 1                 0
  TX                 4                 3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V41, continuous

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    21   3
  9P GAIN WILD-TYPE 116  29
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               24               145 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                29 
$`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         0.82       182.93       134.33 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7X8 TCGA-DS-A3LQ TCGA-DS-A5RQ 
       15.48        73.41        85.55         2.73        22.98        16.83 
TCGA-EA-A5ZE TCGA-EK-A2RN TCGA-EX-A3L1 TCGA-FU-A3TX TCGA-FU-A40J TCGA-IR-A3LL 
       14.99         0.10         6.94         1.48         1.35        36.36 
TCGA-JW-A5VG TCGA-JW-A5VL TCGA-JW-A69B TCGA-LP-A4AU TCGA-MY-A5BE TCGA-UC-A7PD 
       14.43        15.58        10.06         0.10         0.07        11.67 

$`9P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       40.93        44.22        83.05        78.35       100.14        38.43 
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        25.35       101.82 
TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
        9.67        17.19        60.69        94.95         9.34        13.61 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18         7.33         8.28         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
        1.35         1.35        14.50         1.81        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF 
        0.26        14.89         1.48        13.91         0.69        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.58        13.48        12.59        45.96         6.64         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.59         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       23.70         2.24         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
       20.35         7.92        14.70         4.47         6.12         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.58         0.82         3.52         1.32         1.97         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A852 TCGA-LP-A4AW 
       26.56        16.64        19.33        20.48         5.13         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PF 
       93.99 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.07              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           182.93            177.04 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            14.71             13.48 
[1] "0.1 - 182.9 (14.7)" "0.0 - 177.0 (13.5)"
[1] "hr=" "1.8"
D17V2, continuous
                   vv
clus                T1 T2+T3+T4
  9P GAIN MUTATED   12        7
  9P GAIN WILD-TYPE 85       32
D17V3, multiclass
          clus
vv         9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1                    12                85
  T2+T3+T4               7                32
[1] 2 2
[1] FALSE
D17V4, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    9  7
  9P GAIN WILD-TYPE 78 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      9    7
  9P GAIN WILD-TYPE   78   33
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               9                78
  1               7                33
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9P GAIN MUTATED    9  0 10
  9P GAIN WILD-TYPE 63  3 55
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               9                63
  M1               0                 3
  MX              10                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED               0                               21
  9P GAIN WILD-TYPE             2                              123
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9P GAIN MUTATED                                               0
  9P GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9P GAIN MUTATED                                     3
  9P GAIN WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9P GAIN MUTATED                                           0
  9P GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9P GAIN MUTATED                                              1
  9P GAIN WILD-TYPE                                            3
D17V6, multiclass
                                               clus
vv                                              9P GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           21
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              9P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  23
  9P GAIN WILD-TYPE  25 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   23
  9P GAIN WILD-TYPE   25  126
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2                25
  YES              23               126
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  3     2
  9P GAIN WILD-TYPE                                4    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED                           3
  9P GAIN WILD-TYPE                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           0    15
  9P GAIN WILD-TYPE                                         1   115
D17V10, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 4
  ASIAN                                                   2                13
  BLACK OR AFRICAN AMERICAN                               3                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               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"
D17V11, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3  14
  9P GAIN WILD-TYPE   8 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3   14
  9P GAIN WILD-TYPE    8  113
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              14               113
[1] 2 2
[1] FALSE
D17V12, continuous
D17V13, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    7  0
  9P GAIN WILD-TYPE 41 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      7    0
  9P GAIN WILD-TYPE   41   19
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  TUMOR FREE               7                41
  WITH TUMOR               0                19
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  9P GAIN MUTATED         0      0       0            23       2
  9P GAIN WILD-TYPE       1     10       6           124      10
D17V14, multiclass
               clus
vv              9P GAIN MUTATED 9P GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 6
  UNITED STATES              23               124
  VIETNAM                     2                10
[1] 5 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                G1 G2 G3 G4 GX
  9P GAIN MUTATED    1 11 12  0  1
  9P GAIN WILD-TYPE 13 72 60  1  4
D17V15, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  G1               1                13
  G2              11                72
  G3              12                60
  G4               0                 1
  GX               1                 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"
D17V16, continuous
D17V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9P GAIN MUTATED                                             2
  9P GAIN WILD-TYPE                                          19
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  9P GAIN MUTATED                                        2
  9P GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  9P GAIN MUTATED                                                 1
  9P GAIN WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9P GAIN MUTATED                7                  11
  9P GAIN WILD-TYPE             29                  72
D17V18, multiclass
                                                 clus
vv                                                9P GAIN 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                                                7
  LIFELONG NON-SMOKER                                          11
                                                 clus
vv                                                9P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 29
  LIFELONG NON-SMOKER                                            72
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  9P GAIN MUTATED             0        7             2        3
  9P GAIN WILD-TYPE          17       30             9        2
D17V20, multiclass
               clus
vv              9P GAIN MUTATED 9P GAIN WILD-TYPE
  COMBINATION                 0                17
  EXTERNAL                    7                30
  EXTERNAL BEAM               2                 9
  INTERNAL                    3                 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"
D17V21, binary
                   cls
clus                0 1
  9P GAIN MUTATED   3 1
  9P GAIN WILD-TYPE 8 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    1
  9P GAIN WILD-TYPE    8    2
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  CGY               3                 8
  GY                1                 2
[1] 2 2
[1] FALSE
D17V22, continuous
D17V23, continuous
D17V24, continuous
D17V25, continuous
D17V26, continuous
D17V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  9P GAIN MUTATED                                     0
  9P GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  9P GAIN MUTATED                                     0                       3
  9P GAIN WILD-TYPE                                   6                       6
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9P GAIN MUTATED                         0                       0
  9P GAIN WILD-TYPE                       1                       5
D17V28, multiclass
                                     clus
vv                                    9P GAIN MUTATED 9P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           3                 6
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 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)
  9P GAIN MUTATED                                               0
  9P GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  9P GAIN MUTATED                                                1
  9P GAIN WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9P GAIN MUTATED                                                                                   7
  9P GAIN WILD-TYPE                                                                                47
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9P GAIN MUTATED                                                                                             11
  9P GAIN WILD-TYPE                                                                                           66
D17V29, multiclass
                                                                                              clus
vv                                                                                             9P 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)                          7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              11
                                                                                              clus
vv                                                                                             9P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                66
[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"
D17V30, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    6  8
  9P GAIN WILD-TYPE 48 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      6    8
  9P GAIN WILD-TYPE   48   51
         clus
vv        9P GAIN MUTATED 9P GAIN WILD-TYPE
  ABSENT                6                48
  PRESENT               8                51
[1] 2 2
[1] FALSE
D17V31, continuous
D17V32, continuous
D17V33, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    8  7
  9P GAIN WILD-TYPE 27 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      8    7
  9P GAIN WILD-TYPE   27   74
                                          clus
vv                                         9P GAIN MUTATED 9P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   8                27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               7                74
[1] 2 2
[1] FALSE
D17V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  9P GAIN MUTATED       0                   14                   1
  9P GAIN WILD-TYPE     3                   99                   4
D17V35, multiclass
                      clus
vv                     9P GAIN MUTATED 9P GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              14                99
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9P GAIN MUTATED              2           4          4
  9P GAIN WILD-TYPE            6          36         36
D17V36, multiclass
              clus
vv             9P GAIN MUTATED 9P GAIN WILD-TYPE
  CURRENT USER               2                 6
  FORMER USER                4                36
  NEVER USED                 4                36
[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, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    7  0
  9P GAIN WILD-TYPE 66 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      7    0
  9P GAIN WILD-TYPE   66   14
         clus
vv        9P GAIN MUTATED 9P GAIN WILD-TYPE
  ABSENT                7                66
  PRESENT               0                14
[1] 2 2
[1] FALSE
D17V39, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                 8 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1MN        TCGA-EK-A2RO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  9P GAIN MUTATED     0    0   4    4    4  1   2    2    0   1   1  0  0
  9P GAIN WILD-TYPE   2    1  18   47   17  2   4    4    8  12   1  1  7
D17V40, multiclass
      clus
vv     9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                4                18
  T1B1               4                47
  T1B2               4                17
  T2                 1                 2
  T2A                2                 4
  T2A1               2                 4
  T2A2               0                 8
  T2B                1                12
  T3B                1                 1
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V41, continuous

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    20   3
  9Q GAIN WILD-TYPE 117  29
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               23               146 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                29 
$`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       182.93       134.33        15.48 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-DS-A3LQ TCGA-EA-A5ZE TCGA-EK-A2RN TCGA-EX-A3L1 
       73.41        85.55        22.98        14.99         0.10         6.94 
TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VL 
        1.48         3.52         1.35        36.36        14.43        15.58 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-MY-A5BE TCGA-Q1-A6DT TCGA-UC-A7PD 
        5.13         0.10         0.07         3.39        11.67 

$`9Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
       40.93        44.22        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-A7CH 
        0.82        52.01        18.02        17.85        20.42        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
      101.82         9.67        17.19        60.69        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       13.61         2.73        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99       118.65        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        0.76        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05         1.18        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.81        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       13.91         0.69        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       45.96         6.64         0.53         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO 
        0.03         0.36         1.18        23.70         2.24         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 
        0.10         0.10         0.03        20.35         7.92        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        4.47         6.12         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A57G 
        0.66         1.02         1.45         1.58         0.82         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       78.71        81.96        26.56        16.64        19.33        20.48 
TCGA-JW-A69B TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
       10.06         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42        29.72         4.34         2.96         3.72         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        5.85         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PF 
        3.88        93.99 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.07              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           182.93            177.04 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            14.43             13.53 
[1] "0.1 - 182.9 (14.4)" "0.0 - 177.0 (13.5)"
[1] "hr=" "1.8"
D18V2, continuous
                   vv
clus                T1 T2+T3+T4
  9Q GAIN MUTATED   12        7
  9Q GAIN WILD-TYPE 85       32
D18V3, multiclass
          clus
vv         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1                    12                85
  T2+T3+T4               7                32
[1] 2 2
[1] FALSE
D18V4, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   10  7
  9Q GAIN WILD-TYPE 77 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     10    7
  9Q GAIN WILD-TYPE   77   33
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              10                77
  1               7                33
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9Q GAIN MUTATED    9  0 11
  9Q GAIN WILD-TYPE 63  3 54
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               9                63
  M1               0                 3
  MX              11                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED               0                               25
  9Q GAIN WILD-TYPE             2                              119
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9Q GAIN MUTATED                                               0
  9Q GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9Q GAIN MUTATED                                     1
  9Q GAIN WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9Q GAIN MUTATED                                           0
  9Q GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9Q GAIN MUTATED                                              0
  9Q GAIN WILD-TYPE                                            4
D18V6, multiclass
                                               clus
vv                                              9Q GAIN MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           25
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              9Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            119
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  24
  9Q GAIN WILD-TYPE  25 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   24
  9Q GAIN WILD-TYPE   25  125
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                2                25
  YES              24               125
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  3     3
  9Q GAIN WILD-TYPE                                4    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED                           3
  9Q GAIN WILD-TYPE                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           0    15
  9Q GAIN WILD-TYPE                                         1   115
D18V10, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 4
  ASIAN                                                   3                12
  BLACK OR AFRICAN AMERICAN                               3                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               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"
D18V11, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3  14
  9Q GAIN WILD-TYPE   8 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3   14
  9Q GAIN WILD-TYPE    8  113
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 8
  NOT HISPANIC OR LATINO              14               113
[1] 2 2
[1] FALSE
D18V12, continuous
D18V13, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    6  0
  9Q GAIN WILD-TYPE 42 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      6    0
  9Q GAIN WILD-TYPE   42   19
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  TUMOR FREE               6                42
  WITH TUMOR               0                19
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  9Q GAIN MUTATED         0      0       0            23       3
  9Q GAIN WILD-TYPE       1     10       6           124       9
D18V14, multiclass
               clus
vv              9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 6
  UNITED STATES              23               124
  VIETNAM                     3                 9
[1] 5 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                G1 G2 G3 G4 GX
  9Q GAIN MUTATED    2 10 13  0  1
  9Q GAIN WILD-TYPE 12 73 59  1  4
D18V15, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  G1               2                12
  G2              10                73
  G3              13                59
  G4               0                 1
  GX               1                 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"
D18V16, continuous
D18V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9Q GAIN MUTATED                                             1
  9Q GAIN WILD-TYPE                                          20
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  9Q GAIN MUTATED                                        2
  9Q GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  9Q GAIN MUTATED                                                 1
  9Q GAIN WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9Q GAIN MUTATED                6                  13
  9Q GAIN WILD-TYPE             30                  70
D18V18, multiclass
                                                 clus
vv                                                9Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               1
  CURRENT SMOKER                                                6
  LIFELONG NON-SMOKER                                          13
                                                 clus
vv                                                9Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 30
  LIFELONG NON-SMOKER                                            70
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  9Q GAIN MUTATED             0        5             2        3
  9Q GAIN WILD-TYPE          17       32             9        2
D18V20, multiclass
               clus
vv              9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COMBINATION                 0                17
  EXTERNAL                    5                32
  EXTERNAL BEAM               2                 9
  INTERNAL                    3                 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"
D18V21, binary
                   cls
clus                0 1
  9Q GAIN MUTATED   3 1
  9Q GAIN WILD-TYPE 8 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    1
  9Q GAIN WILD-TYPE    8    2
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CGY               3                 8
  GY                1                 2
[1] 2 2
[1] FALSE
D18V22, continuous
D18V23, continuous
D18V24, continuous
D18V25, continuous
D18V26, continuous
D18V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  9Q GAIN MUTATED                                     0
  9Q GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  9Q GAIN MUTATED                                     0                       3
  9Q GAIN WILD-TYPE                                   6                       6
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9Q GAIN MUTATED                         0                       0
  9Q GAIN WILD-TYPE                       1                       5
D18V28, multiclass
                                     clus
vv                                    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               0                 6
  OTHER LOCATION, SPECIFY                           3                 6
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           0                 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)
  9Q GAIN MUTATED                                               0
  9Q GAIN WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  9Q GAIN MUTATED                                                1
  9Q GAIN WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9Q GAIN MUTATED                                                                                   7
  9Q GAIN WILD-TYPE                                                                                47
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9Q GAIN MUTATED                                                                                             12
  9Q GAIN WILD-TYPE                                                                                           65
D18V29, multiclass
                                                                                              clus
vv                                                                                             9Q 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)                          7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              12
                                                                                              clus
vv                                                                                             9Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                65
[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"
D18V30, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    6  6
  9Q GAIN WILD-TYPE 48 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      6    6
  9Q GAIN WILD-TYPE   48   53
         clus
vv        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ABSENT                6                48
  PRESENT               6                53
[1] 2 2
[1] FALSE
D18V31, continuous
D18V32, continuous
D18V33, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    8 10
  9Q GAIN WILD-TYPE 27 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      8   10
  9Q GAIN WILD-TYPE   27   71
                                          clus
vv                                         9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   8                27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              10                71
[1] 2 2
[1] FALSE
D18V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  9Q GAIN MUTATED       0                   14                   1
  9Q GAIN WILD-TYPE     3                   99                   4
D18V35, multiclass
                      clus
vv                     9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              14                99
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9Q GAIN MUTATED              2           4          3
  9Q GAIN WILD-TYPE            6          36         37
D18V36, multiclass
              clus
vv             9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  CURRENT USER               2                 6
  FORMER USER                4                36
  NEVER USED                 3                37
[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, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    6  0
  9Q GAIN WILD-TYPE 67 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      6    0
  9Q GAIN WILD-TYPE   67   14
         clus
vv        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ABSENT                6                67
  PRESENT               0                14
[1] 2 2
[1] FALSE
D18V39, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                 7 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1MN        TCGA-EK-A2RO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-MU-A51Y        TCGA-MU-A8JM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  9Q GAIN MUTATED     0    0   5    4    3  1   1    2    0   2   1  0  1
  9Q GAIN WILD-TYPE   2    1  17   47   18  2   5    4    8  11   1  1  6
D18V40, multiclass
      clus
vv     9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                5                17
  T1B1               4                47
  T1B2               3                18
  T2                 1                 2
  T2A                1                 5
  T2A1               2                 4
  T2A2               0                 8
  T2B                2                11
  T3B                1                 1
  T4                 0                 1
  TX                 1                 6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V41, continuous

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    10   4
  10P GAIN WILD-TYPE 127  28
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                155 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 28 
$`10P GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LZ TCGA-C5-A7CH 
       57.04       173.29        35.01        57.73       100.14        25.35 
TCGA-C5-A7X5 TCGA-DS-A0VK TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-FU-A3NI TCGA-HM-A4S6 
       13.61        36.76         0.53         1.18         1.45        14.93 
TCGA-IR-A3LL TCGA-LP-A4AW 
       36.36         0.89 

$`10P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        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-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       31.40        46.32        30.21        53.16        38.99        35.61 
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-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.45        83.05        78.35        38.43         0.82        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       182.93       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48         9.67        73.41        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       94.95         9.34         2.73        87.75        58.88         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50         1.81        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB 
       13.48        12.59        45.96         6.64         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        4.04         0.03         0.36        23.70         2.24         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70         4.47         6.12         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17         0.66         1.02         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       25.41        21.67        20.78         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       14.43        16.64        19.33        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        5.13         0.10         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         2.96         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.45         5.85         3.39         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        19.59         3.88        11.67        93.99 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.53               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            173.29             182.93 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             30.18              12.82 
[1] "0.5 - 173.3 (30.2)" "0.0 - 182.9 (12.8)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 T1 T2+T3+T4
  10P GAIN MUTATED    9        1
  10P GAIN WILD-TYPE 88       38
D19V3, multiclass
          clus
vv         10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                      9                 88
  T2+T3+T4                1                 38
[1] 2 2
[1] FALSE
D19V4, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    5  5
  10P GAIN WILD-TYPE 82 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    5
  10P GAIN WILD-TYPE   82   35
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                5                 82
  1                5                 35
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10P GAIN MUTATED    7  0  3
  10P GAIN WILD-TYPE 65  3 62
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                7                 65
  M1                0                  3
  MX                3                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED               0                               12
  10P GAIN WILD-TYPE             2                              132
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10P GAIN MUTATED                                               0
  10P GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10P GAIN MUTATED                                     2
  10P GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10P GAIN MUTATED                                           0
  10P GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10P GAIN MUTATED                                              0
  10P GAIN WILD-TYPE                                            4
D19V6, multiclass
                                               clus
vv                                              10P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            12
  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                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             132
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2  12
  10P GAIN WILD-TYPE  25 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   12
  10P GAIN WILD-TYPE   25  137
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                 25
  YES               12                137
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     1
  10P GAIN WILD-TYPE                                7    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED                           2
  10P GAIN WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           0    11
  10P GAIN WILD-TYPE                                         1   119
D19V10, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    1                 14
  BLACK OR AFRICAN AMERICAN                                2                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                119
[1] 5 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     0  12
  10P GAIN WILD-TYPE  11 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   12
  10P GAIN WILD-TYPE   11  115
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               12                115
[1] 2 2
[1] FALSE
D19V12, continuous
D19V13, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    5  2
  10P GAIN WILD-TYPE 43 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    2
  10P GAIN WILD-TYPE   43   17
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  TUMOR FREE                5                 43
  WITH TUMOR                2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  10P GAIN MUTATED         0      0       0            13       1
  10P GAIN WILD-TYPE       1     10       6           134      11
D19V14, multiclass
               clus
vv              10P GAIN MUTATED 10P GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      0                  6
  UNITED STATES               13                134
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  10P GAIN MUTATED    2  5  7  0  0
  10P GAIN WILD-TYPE 12 78 65  1  5
D19V15, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  G1                2                 12
  G2                5                 78
  G3                7                 65
  G4                0                  1
  GX                0                  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"
D19V16, continuous
D19V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10P GAIN MUTATED                                             3
  10P GAIN WILD-TYPE                                          18
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  10P GAIN MUTATED                                        1
  10P GAIN WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  10P GAIN MUTATED                                                 0
  10P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10P GAIN MUTATED                3                   4
  10P GAIN WILD-TYPE             33                  79
D19V18, multiclass
                                                 clus
vv                                                10P GAIN 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                                                 3
  LIFELONG NON-SMOKER                                            4
                                                 clus
vv                                                10P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  33
  LIFELONG NON-SMOKER                                             79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  10P GAIN MUTATED             1        4             2        0
  10P GAIN WILD-TYPE          16       33             9        5
D19V20, multiclass
               clus
vv              10P GAIN MUTATED 10P GAIN WILD-TYPE
  COMBINATION                  1                 16
  EXTERNAL                     4                 33
  EXTERNAL BEAM                2                  9
  INTERNAL                     0                  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"
D19V21, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  0
  10P GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    0
  10P GAIN WILD-TYPE   10    3
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D19V22, continuous
D19V23, continuous
D19V24, continuous
D19V25, continuous
D19V26, continuous
D19V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  10P GAIN MUTATED                                     0
  10P GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  10P GAIN MUTATED                                     0
  10P GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  10P GAIN MUTATED                         1                       0
  10P GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10P GAIN MUTATED                         1
  10P GAIN WILD-TYPE                       4
D19V28, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 21 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A2LX         TCGA-DR-A0ZM 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-EA-A50E         TCGA-EK-A2RN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-EX-A1H5         TCGA-EX-A449 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-IR-A3LH         TCGA-IR-A3LI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A8JM         TCGA-UC-A7PD 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
                    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                                                1
  10P GAIN WILD-TYPE                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10P GAIN MUTATED                                                                                   3
  10P GAIN WILD-TYPE                                                                                51
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10P GAIN MUTATED                                                                                              7
  10P GAIN WILD-TYPE                                                                                           70
D19V29, multiclass
                                                                                              clus
vv                                                                                             10P 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)                           3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                7
                                                                                              clus
vv                                                                                             10P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                9
  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)                 70
[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"
D19V30, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  7
  10P GAIN WILD-TYPE 52 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    7
  10P GAIN WILD-TYPE   52   52
         clus
vv        10P GAIN MUTATED 10P GAIN WILD-TYPE
  ABSENT                 2                 52
  PRESENT                7                 52
[1] 2 2
[1] FALSE
D19V31, continuous
D19V32, continuous
D19V33, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    6  3
  10P GAIN WILD-TYPE 29 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    3
  10P GAIN WILD-TYPE   29   78
                                          clus
vv                                         10P GAIN MUTATED 10P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                3                 78
[1] 2 2
[1] FALSE
D19V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  10P GAIN MUTATED       0                    9                   0
  10P GAIN WILD-TYPE     3                  104                   5
D19V35, multiclass
                      clus
vv                     10P GAIN MUTATED 10P GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY                9                104
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10P GAIN MUTATED              0           3          2
  10P GAIN WILD-TYPE            8          37         38
D19V36, multiclass
              clus
vv             10P GAIN MUTATED 10P GAIN WILD-TYPE
  CURRENT USER                0                  8
  FORMER USER                 3                 37
  NEVER USED                  2                 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"
D19V37, continuous
D19V38, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    6  0
  10P GAIN WILD-TYPE 67 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    0
  10P GAIN WILD-TYPE   67   14
         clus
vv        10P GAIN MUTATED 10P GAIN WILD-TYPE
  ABSENT                 6                 67
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D19V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  10P GAIN MUTATED     1    0   1    5    2  0   0    0    0   0   1  0  0
  10P GAIN WILD-TYPE   1    1  21   46   19  3   6    6    8  13   1  1  7
D19V40, multiclass
      clus
vv     10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1A                 1                  1
  T1A1                0                  1
  T1B                 1                 21
  T1B1                5                 46
  T1B2                2                 19
  T2                  0                  3
  T2A                 0                  6
  T2A1                0                  6
  T2A2                0                  8
  T2B                 0                 13
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V41, continuous

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     6   2
  10Q GAIN WILD-TYPE 131  30
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 8                161 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 30 
$`10Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LZ TCGA-C5-A7CH TCGA-EK-A2PG 
       57.04        35.01        57.73       100.14        25.35         0.53 
TCGA-IR-A3LL TCGA-LP-A4AU 
       36.36         0.10 

$`10Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        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-A1MF TCGA-C5-A1MH 
       67.46        31.40        46.32        30.21        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       35.61         0.46         2.43        40.93         3.58        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         0.82 
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       182.93       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48         9.67        73.41        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL 
       60.69        94.95         9.34        13.61         2.73        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18         7.33         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         0.26        14.89         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        6.64         0.59         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        23.70         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        4.47         6.12         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.66         1.02         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         1.12        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         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       14.43        16.64        19.33        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        5.13         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         2.96         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.45         5.85         3.39         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        6.25        19.59         3.88        11.67        93.99 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.10               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            100.14             182.93 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            35.685             13.050 
[1] "0.1 - 100.1 (35.7)" "0.0 - 182.9 (13.1)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 T1 T2+T3+T4
  10Q GAIN MUTATED    3        2
  10Q GAIN WILD-TYPE 94       37
D20V3, multiclass
          clus
vv         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                      3                 94
  T2+T3+T4                2                 37
[1] 2 2
[1] FALSE
D20V4, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  2
  10Q GAIN WILD-TYPE 84 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    2
  10Q GAIN WILD-TYPE   84   38
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                3                 84
  1                2                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10Q GAIN MUTATED    5  0  0
  10Q GAIN WILD-TYPE 67  3 65
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                5                 67
  M1                0                  3
  MX                0                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED               0                                6
  10Q GAIN WILD-TYPE             2                              138
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10Q GAIN MUTATED                                               0
  10Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10Q GAIN MUTATED                                     2
  10Q GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10Q GAIN MUTATED                                           0
  10Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10Q GAIN MUTATED                                              0
  10Q GAIN WILD-TYPE                                            4
D20V6, multiclass
                                               clus
vv                                              10Q 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                                              10Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             138
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   7
  10Q GAIN WILD-TYPE  26 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    7
  10Q GAIN WILD-TYPE   26  142
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                 26
  YES                7                142
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1MF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2M2         TCGA-C5-A3HD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A7UI         TCGA-C5-A7X8         TCGA-DR-A0ZM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-EA-A556 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JW-A5VI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-MU-A5YI         TCGA-MU-A8JM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741         TCGA-UC-A7PD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     1
  10Q GAIN WILD-TYPE                                7    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED                           1
  10Q GAIN WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           0     6
  10Q GAIN WILD-TYPE                                         1   124
D20V10, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    1                 14
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                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"
D20V11, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0   6
  10Q GAIN WILD-TYPE  11 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    6
  10Q GAIN WILD-TYPE   11  121
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                6                121
[1] 2 2
[1] FALSE
D20V12, continuous
D20V13, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  2
  10Q GAIN WILD-TYPE 45 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    2
  10Q GAIN WILD-TYPE   45   17
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  TUMOR FREE                3                 45
  WITH TUMOR                2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  10Q GAIN MUTATED         0      0       0             7       1
  10Q GAIN WILD-TYPE       1     10       6           140      11
D20V14, multiclass
               clus
vv              10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      0                  6
  UNITED STATES                7                140
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  10Q GAIN MUTATED    1  3  4  0  0
  10Q GAIN WILD-TYPE 13 80 68  1  5
D20V15, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  G1                1                 13
  G2                3                 80
  G3                4                 68
  G4                0                  1
  GX                0                  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"
D20V16, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 24 
        TCGA-BI-A0VR         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1MF         TCGA-C5-A1MH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A7CM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-DS-A3LQ         TCGA-EX-A69M 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3TX         TCGA-FU-A3WB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-HM-A4S6         TCGA-IR-A3L7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-MU-A5YI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V17, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1MF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2M2         TCGA-C5-A3HD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A7UI         TCGA-C5-A7X8         TCGA-DR-A0ZM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-EA-A556 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JW-A5VI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-MU-A5YI         TCGA-MU-A8JM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741         TCGA-UC-A7PD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10Q GAIN MUTATED                                             1
  10Q GAIN WILD-TYPE                                          20
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  10Q GAIN MUTATED                                        0
  10Q GAIN WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  10Q GAIN MUTATED                                                 0
  10Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10Q GAIN MUTATED                2                   4
  10Q GAIN WILD-TYPE             34                  79
D20V18, multiclass
                                                 clus
vv                                                10Q 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                                            4
                                                 clus
vv                                                10Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  34
  LIFELONG NON-SMOKER                                             79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V19, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 46 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1MF         TCGA-C5-A1MI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2M2         TCGA-C5-A3HD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A7CJ         TCGA-C5-A7CL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7X8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-EA-A556 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3TX 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-HM-A4S6         TCGA-HM-A6W2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VK         TCGA-MU-A5YI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD 
"10Q GAIN WILD-TYPE" 
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  10Q GAIN MUTATED             0        2             1        0
  10Q GAIN WILD-TYPE          17       35            10        5
D20V20, multiclass
               clus
vv              10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COMBINATION                  0                 17
  EXTERNAL                     2                 35
  EXTERNAL BEAM                1                 10
  INTERNAL                     0                  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"
D20V21, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    0  0
  10Q GAIN WILD-TYPE 11  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    0
  10Q GAIN WILD-TYPE   11    3
D20V22, continuous
D20V23, continuous
D20V24, continuous
D20V25, continuous
D20V26, continuous
D20V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  10Q GAIN MUTATED                                     0
  10Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  10Q GAIN MUTATED                                     0
  10Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  10Q GAIN MUTATED                         0                       0
  10Q GAIN WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10Q GAIN MUTATED                         0
  10Q GAIN WILD-TYPE                       5
D20V28, multiclass
                    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                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10Q GAIN MUTATED                                                                                   3
  10Q GAIN WILD-TYPE                                                                                51
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10Q GAIN MUTATED                                                                                              4
  10Q GAIN WILD-TYPE                                                                                           73
D20V29, 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)                           3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                4
                                                                                              clus
vv                                                                                             10Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  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)                 73
[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"
D20V30, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  2
  10Q GAIN WILD-TYPE 52 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    2
  10Q GAIN WILD-TYPE   52   57
         clus
vv        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ABSENT                 2                 52
  PRESENT                2                 57
[1] 2 2
[1] FALSE
D20V31, continuous
D20V32, continuous
D20V33, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  1
  10Q GAIN WILD-TYPE 33 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    1
  10Q GAIN WILD-TYPE   33   80
                                          clus
vv                                         10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    2                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                1                 80
[1] 2 2
[1] FALSE
D20V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  10Q GAIN MUTATED       0                    4                   1
  10Q GAIN WILD-TYPE     3                  109                   4
D20V35, multiclass
                      clus
vv                     10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY                4                109
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10Q GAIN MUTATED              0           2          0
  10Q GAIN WILD-TYPE            8          38         40
D20V36, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 86 
        TCGA-C5-A1BI         TCGA-C5-A1BL         TCGA-C5-A1BN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1M6         TCGA-C5-A1M7         TCGA-C5-A1M8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MN         TCGA-C5-A2LT 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A2M2         TCGA-C5-A3HD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7UH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-C5-A7X3         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-DS-A7WF 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DS-A7WH         TCGA-DS-A7WI         TCGA-EA-A1QS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A3QD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A410         TCGA-EA-A411 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EA-A44S         TCGA-EA-A4BA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EA-A556         TCGA-EA-A5O9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EA-A5ZE         TCGA-EA-A5ZF         TCGA-EK-A2R7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EK-A3GK         TCGA-EX-A1H5         TCGA-EX-A1H6 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-EX-A69L         TCGA-EX-A69M 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A57G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-HM-A3JJ         TCGA-HM-A3JK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IR-A3LA         TCGA-IR-A3LB         TCGA-IR-A3LC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-IR-A3LI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-JW-A5VG         TCGA-JW-A5VI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A69B 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-LP-A5U3         TCGA-PN-A8MA         TCGA-Q1-A5R1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Q1-A5R2         TCGA-Q1-A5R3         TCGA-Q1-A6DV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Q1-A73P         TCGA-UC-A7PD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V37, continuous
D20V38, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  0
  10Q GAIN WILD-TYPE 70 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    0
  10Q GAIN WILD-TYPE   70   14
         clus
vv        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ABSENT                 3                 70
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D20V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  10Q GAIN MUTATED     0    0   0    3    0  1   0    0    0   0   1  0  0
  10Q GAIN WILD-TYPE   2    1  22   48   21  2   6    6    8  13   1  1  7
D20V40, multiclass
      clus
vv     10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 0                 22
  T1B1                3                 48
  T1B2                0                 21
  T2                  1                  2
  T2A                 0                  6
  T2A1                0                  6
  T2A2                0                  8
  T2B                 0                 13
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V41, continuous

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     3   1
  11P GAIN WILD-TYPE 134  31
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                165 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 31 
$`11P GAIN MUTATED`
TCGA-C5-A1M9 TCGA-C5-A2LT TCGA-EX-A3L1 TCGA-FU-A40J 
       35.01        73.18         6.94         1.35 

$`11P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       53.16        38.99        35.61         0.46         2.43        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         0.82        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 
      182.93        25.35       101.82       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       73.41        17.19        85.55        60.69        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       13.61         2.73        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50         1.81        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
       20.35         7.92        14.70         4.47         6.12         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        25.41        21.67        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.35               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             73.18             182.93 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            20.975             13.580 
[1] "1.4 - 73.2 (21.0)"  "0.0 - 182.9 (13.6)"
[1] "hr=" "1.3"
D21V2, continuous
                    vv
clus                 T1 T2+T3+T4
  11P GAIN MUTATED    1        3
  11P GAIN WILD-TYPE 96       36
D21V3, multiclass
          clus
vv         11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                      1                 96
  T2+T3+T4                3                 36
[1] 2 2
[1] FALSE
D21V4, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  2
  11P GAIN WILD-TYPE 85 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    2
  11P GAIN WILD-TYPE   85   38
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                2                 85
  1                2                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11P GAIN MUTATED    3  0  1
  11P GAIN WILD-TYPE 69  3 64
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                3                 69
  M1                0                  3
  MX                1                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED               0                                3
  11P GAIN WILD-TYPE             2                              141
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11P GAIN MUTATED                                               0
  11P GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11P GAIN MUTATED                                     2
  11P GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11P GAIN MUTATED                                           0
  11P GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11P GAIN MUTATED                                              0
  11P GAIN WILD-TYPE                                            4
D21V6, multiclass
                                               clus
vv                                              11P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             3
  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                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             141
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2   3
  11P GAIN WILD-TYPE  25 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    3
  11P GAIN WILD-TYPE   25  146
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 2                 25
  YES                3                146
[1] 2 2
[1] FALSE
D21V8, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 52 
        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-A1MN         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-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UI         TCGA-C5-A7X8 
"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-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-MU-A5YI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PD 
"11P GAIN WILD-TYPE" 
D21V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                7    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED                           0
  11P GAIN WILD-TYPE                        18
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           0     5
  11P GAIN WILD-TYPE                                         1   125
D21V10, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    0                 15
  BLACK OR AFRICAN AMERICAN                                0                 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                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"
D21V11, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0   4
  11P GAIN WILD-TYPE  11 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    4
  11P GAIN WILD-TYPE   11  123
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                4                123
[1] 2 2
[1] FALSE
D21V12, continuous
D21V13, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    1  1
  11P GAIN WILD-TYPE 47 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    1
  11P GAIN WILD-TYPE   47   18
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  TUMOR FREE                1                 47
  WITH TUMOR                1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  11P GAIN MUTATED         0      0       0             5       0
  11P GAIN WILD-TYPE       1     10       6           142      12
D21V14, multiclass
               clus
vv              11P GAIN MUTATED 11P GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      0                  6
  UNITED STATES                5                142
  VIETNAM                      0                 12
[1] 5 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                 G1 G2 G3 G4 GX
  11P GAIN MUTATED    0  1  4  0  0
  11P GAIN WILD-TYPE 14 82 68  1  5
D21V15, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  G1                0                 14
  G2                1                 82
  G3                4                 68
  G4                0                  1
  GX                0                  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"
D21V16, continuous
D21V17, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 52 
        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-A1MN         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-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UI         TCGA-C5-A7X8 
"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-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-MU-A5YI 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PD 
"11P GAIN WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11P GAIN MUTATED                                             0
  11P GAIN WILD-TYPE                                          21
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  11P GAIN MUTATED                                        0
  11P GAIN WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  11P GAIN MUTATED                                                 0
  11P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11P GAIN MUTATED                1                   3
  11P GAIN WILD-TYPE             35                  80
D21V18, 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                0
  CURRENT SMOKER                                                 1
  LIFELONG NON-SMOKER                                            3
                                                 clus
vv                                                11P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  35
  LIFELONG NON-SMOKER                                             80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V19, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 47 
        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-DR-A0ZM         TCGA-DS-A5RQ 
"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-A3TX         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A5XV         TCGA-FU-A770         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-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  11P GAIN MUTATED             0        1             2        0
  11P GAIN WILD-TYPE          17       36             9        5
D21V20, multiclass
               clus
vv              11P GAIN MUTATED 11P GAIN WILD-TYPE
  COMBINATION                  0                 17
  EXTERNAL                     1                 36
  EXTERNAL BEAM                2                  9
  INTERNAL                     0                  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"
D21V21, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    1  0
  11P GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    0
  11P GAIN WILD-TYPE   10    3
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D21V22, continuous
D21V23, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 91 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         TCGA-C5-A1M6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         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-A1MJ         TCGA-C5-A1MK         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-DR-A0ZL         TCGA-DS-A0VK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HS         TCGA-EA-A3HT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3QE         TCGA-EA-A3Y4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A44S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-EX-A449 
"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-A3HZ         TCGA-FU-A3TQ         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-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-RA-A741         TCGA-UC-A7PD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PF 
"11P GAIN WILD-TYPE" 
D21V24, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                103 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BF         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BL         TCGA-C5-A1BM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1BQ         TCGA-C5-A1M5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M6         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-A1MH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MJ         TCGA-C5-A1MK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-C5-A2LS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A2M1         TCGA-C5-A2M2 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HE         TCGA-C5-A3HF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CH 
"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-A7UH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A7UI         TCGA-C5-A7X3         TCGA-C5-A7X8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DR-A0ZM         TCGA-DS-A0VK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EA-A3QD         TCGA-EA-A3QE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3Y4         TCGA-EA-A410         TCGA-EA-A411 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A556         TCGA-EA-A5O9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A5ZD         TCGA-EK-A2IP         TCGA-EK-A2RK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EX-A69L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3TQ 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A57G         TCGA-FU-A770 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK         TCGA-HM-A4S6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LC         TCGA-IR-A3LF 
"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-IR-A3LL         TCGA-JW-A5VG         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-MU-A8JM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-PN-A8MA         TCGA-RA-A741         TCGA-UC-A7PD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PF 
"11P GAIN WILD-TYPE" 
D21V25, continuous
D21V26, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 98 
        TCGA-BI-A0VS         TCGA-C5-A0TN         TCGA-C5-A1BE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         TCGA-C5-A1M6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         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-A1MJ         TCGA-C5-A1MK         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-DR-A0ZL         TCGA-DS-A0VK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EA-A3QD         TCGA-EA-A3QE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3Y4         TCGA-EA-A410         TCGA-EA-A411 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A556 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EA-A6QX         TCGA-EK-A2RN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EX-A1H6         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-A3JJ         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-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-MU-A51Y         TCGA-RA-A741 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D21V27, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 92 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         TCGA-C5-A1M6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         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-A1MJ         TCGA-C5-A1MK         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-DR-A0ZL         TCGA-DS-A0VK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HS         TCGA-EA-A3HT 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3QE         TCGA-EA-A3Y4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A44S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-EX-A69M 
"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-A3HZ         TCGA-FU-A3TQ         TCGA-FU-A5XV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-HG-A2PA         TCGA-HM-A3JK 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LC         TCGA-IR-A3LF 
"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-IR-A3LL         TCGA-JW-A5VG         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-RA-A741 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  11P GAIN MUTATED                                     0
  11P GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  11P GAIN MUTATED                                     0
  11P GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  11P GAIN MUTATED                         0                       0
  11P GAIN WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11P GAIN MUTATED                         0
  11P GAIN WILD-TYPE                       5
D21V28, multiclass
                    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                                                0
  11P GAIN WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11P GAIN MUTATED                                                                                   0
  11P GAIN WILD-TYPE                                                                                54
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11P GAIN MUTATED                                                                                              4
  11P GAIN WILD-TYPE                                                                                           73
D21V29, multiclass
                                                                                              clus
vv                                                                                             11P 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)                4
                                                                                              clus
vv                                                                                             11P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  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)                 73
[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"
D21V30, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  2
  11P GAIN WILD-TYPE 52 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    2
  11P GAIN WILD-TYPE   52   57
         clus
vv        11P GAIN MUTATED 11P GAIN WILD-TYPE
  ABSENT                 2                 52
  PRESENT                2                 57
[1] 2 2
[1] FALSE
D21V31, continuous
D21V32, continuous
D21V33, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    1  1
  11P GAIN WILD-TYPE 34 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    1
  11P GAIN WILD-TYPE   34   80
                                          clus
vv                                         11P GAIN MUTATED 11P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    1                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                1                 80
[1] 2 2
[1] FALSE
D21V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  11P GAIN MUTATED       0                    3                   0
  11P GAIN WILD-TYPE     3                  110                   5
D21V35, multiclass
                      clus
vv                     11P GAIN MUTATED 11P GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY                3                110
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11P GAIN MUTATED              2           1          0
  11P GAIN WILD-TYPE            6          39         40
D21V36, multiclass
              clus
vv             11P GAIN MUTATED 11P GAIN WILD-TYPE
  CURRENT USER                2                  6
  FORMER USER                 1                 39
  NEVER USED                  0                 40
[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
D21V38, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  0
  11P GAIN WILD-TYPE 69 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    0
  11P GAIN WILD-TYPE   69   14
         clus
vv        11P GAIN MUTATED 11P GAIN WILD-TYPE
  ABSENT                 4                 69
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D21V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  11P GAIN MUTATED     0    0   1    0    0  0   0    2    0   0   1  0  0
  11P GAIN WILD-TYPE   2    1  21   51   21  3   6    4    8  13   1  1  7
D21V40, multiclass
      clus
vv     11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 1                 21
  T1B1                0                 51
  T1B2                0                 21
  T2                  0                  3
  T2A                 0                  6
  T2A1                2                  4
  T2A2                0                  8
  T2B                 0                 13
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V41, continuous

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     4   1
  11Q GAIN WILD-TYPE 133  31
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                164 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 31 
$`11Q GAIN MUTATED`
TCGA-C5-A1M9 TCGA-C5-A2LT TCGA-EK-A2RJ TCGA-EX-A3L1 TCGA-FU-A40J 
       35.01        73.18         1.18         6.94         1.35 

$`11Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       53.16        38.99        35.61         0.46         2.43        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         0.82        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 
      182.93        25.35       101.82       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       73.41        17.19        85.55        60.69        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       13.61         2.73        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50         1.81        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         4.04         0.03         0.36        23.70         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        7.92        14.70         4.47         6.12         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.32         1.97         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36        14.43        16.64        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       15.58        10.06         5.13         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.18               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             73.18             182.93 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             6.940             13.595 
[1] "1.2 - 73.2 (6.9)"   "0.0 - 182.9 (13.6)"
[1] "hr=" "1.3"
D22V2, continuous
                    vv
clus                 T1 T2+T3+T4
  11Q GAIN MUTATED    2        3
  11Q GAIN WILD-TYPE 95       36
D22V3, multiclass
          clus
vv         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                      2                 95
  T2+T3+T4                3                 36
[1] 2 2
[1] FALSE
D22V4, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  2
  11Q GAIN WILD-TYPE 84 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    2
  11Q GAIN WILD-TYPE   84   38
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                3                 84
  1                2                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11Q GAIN MUTATED    3  0  2
  11Q GAIN WILD-TYPE 69  3 63
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                3                 69
  M1                0                  3
  MX                2                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED               0                                3
  11Q GAIN WILD-TYPE             2                              141
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11Q GAIN MUTATED                                               0
  11Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11Q GAIN MUTATED                                     2
  11Q GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11Q GAIN MUTATED                                           0
  11Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11Q GAIN MUTATED                                              0
  11Q GAIN WILD-TYPE                                            4
D22V6, multiclass
                                               clus
vv                                              11Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             3
  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                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             141
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     2   3
  11Q GAIN WILD-TYPE  25 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    3
  11Q GAIN WILD-TYPE   25  146
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 2                 25
  YES                3                146
[1] 2 2
[1] FALSE
D22V8, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 52 
        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-A1MN         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-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UI         TCGA-C5-A7X8 
"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-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-MU-A5YI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD 
"11Q GAIN WILD-TYPE" 
D22V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                7    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED                           0
  11Q GAIN WILD-TYPE                        18
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           0     5
  11Q GAIN WILD-TYPE                                         1   125
D22V10, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    0                 15
  BLACK OR AFRICAN AMERICAN                                0                 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    5                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"
D22V11, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0   5
  11Q GAIN WILD-TYPE  11 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    5
  11Q GAIN WILD-TYPE   11  122
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                5                122
[1] 2 2
[1] FALSE
D22V12, continuous
D22V13, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1  1
  11Q GAIN WILD-TYPE 47 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    1
  11Q GAIN WILD-TYPE   47   18
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  TUMOR FREE                1                 47
  WITH TUMOR                1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  11Q GAIN MUTATED         0      0       0             5       0
  11Q GAIN WILD-TYPE       1     10       6           142      12
D22V14, multiclass
               clus
vv              11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      0                  6
  UNITED STATES                5                142
  VIETNAM                      0                 12
[1] 5 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                 G1 G2 G3 G4 GX
  11Q GAIN MUTATED    0  0  5  0  0
  11Q GAIN WILD-TYPE 14 83 67  1  5
D22V15, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  G1                0                 14
  G2                0                 83
  G3                5                 67
  G4                0                  1
  GX                0                  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"
D22V16, continuous
D22V17, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 52 
        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-A1MN         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-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UI         TCGA-C5-A7X8 
"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-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-MU-A5YI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD 
"11Q GAIN WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11Q GAIN MUTATED                                             0
  11Q GAIN WILD-TYPE                                          21
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  11Q GAIN MUTATED                                        0
  11Q GAIN WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  11Q GAIN MUTATED                                                 0
  11Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11Q GAIN MUTATED                1                   3
  11Q GAIN WILD-TYPE             35                  80
D22V18, 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                0
  CURRENT SMOKER                                                 1
  LIFELONG NON-SMOKER                                            3
                                                 clus
vv                                                11Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  35
  LIFELONG NON-SMOKER                                             80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V19, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 47 
        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-DR-A0ZM         TCGA-DS-A5RQ 
"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-A3TX         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A5XV         TCGA-FU-A770         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-MU-A5YI         TCGA-MU-A8JM         TCGA-Q1-A6DW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  11Q GAIN MUTATED             0        1             2        0
  11Q GAIN WILD-TYPE          17       36             9        5
D22V20, multiclass
               clus
vv              11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COMBINATION                  0                 17
  EXTERNAL                     1                 36
  EXTERNAL BEAM                2                  9
  INTERNAL                     0                  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"
D22V21, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1  0
  11Q GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    0
  11Q GAIN WILD-TYPE   10    3
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D22V22, continuous
D22V23, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 91 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         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-A1MH         TCGA-C5-A1MI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MJ         TCGA-C5-A1MK         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-DR-A0ZL         TCGA-DS-A0VK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         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-A3Y4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A44S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-EX-A449 
"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-A3HZ         TCGA-FU-A3TQ         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-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-RA-A741         TCGA-UC-A7PD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PF 
"11Q GAIN WILD-TYPE" 
D22V24, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                103 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BF         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BL         TCGA-C5-A1BM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1BQ         TCGA-C5-A1M5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1M6         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-A1MH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MJ         TCGA-C5-A1MK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A1MP         TCGA-C5-A2LS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A2M1         TCGA-C5-A2M2 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HE         TCGA-C5-A3HF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CG         TCGA-C5-A7CH 
"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-A7UH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A7UI         TCGA-C5-A7X3         TCGA-C5-A7X8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DR-A0ZM         TCGA-DS-A0VK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EA-A3QD         TCGA-EA-A3QE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3Y4         TCGA-EA-A410         TCGA-EA-A411 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A556         TCGA-EA-A5O9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A5ZD         TCGA-EK-A2IP         TCGA-EK-A2RK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EX-A69L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3TQ 
"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-A2PA         TCGA-HM-A3JK         TCGA-HM-A4S6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LC         TCGA-IR-A3LF 
"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-IR-A3LL         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-A5VL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-MU-A8JM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-PN-A8MA         TCGA-RA-A741         TCGA-UC-A7PD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PF 
"11Q GAIN WILD-TYPE" 
D22V25, continuous
D22V26, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 98 
        TCGA-BI-A0VS         TCGA-C5-A0TN         TCGA-C5-A1BE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         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-A1MH         TCGA-C5-A1MI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MJ         TCGA-C5-A1MK         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-DR-A0ZL         TCGA-DS-A0VK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EA-A3QD         TCGA-EA-A3QE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3Y4         TCGA-EA-A410         TCGA-EA-A411 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A556 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EA-A6QX         TCGA-EK-A2RN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EX-A1H6         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-A3JJ         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-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-MU-A51Y         TCGA-RA-A741 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D22V27, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 92 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         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-A1MH         TCGA-C5-A1MI 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-C5-A1MJ         TCGA-C5-A1MK         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-DR-A0ZL         TCGA-DS-A0VK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         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-A3Y4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A44S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-EX-A69M 
"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-A3HZ         TCGA-FU-A3TQ         TCGA-FU-A5XV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-HG-A2PA         TCGA-HM-A3JK 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LC         TCGA-IR-A3LF 
"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-IR-A3LL         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-A5VL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-RA-A741 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD         TCGA-UC-A7PF 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  11Q GAIN MUTATED                                     0
  11Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  11Q GAIN MUTATED                                     0
  11Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  11Q GAIN MUTATED                         0                       0
  11Q GAIN WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11Q GAIN MUTATED                         0
  11Q GAIN WILD-TYPE                       5
D22V28, multiclass
                    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                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11Q GAIN MUTATED                                                                                   0
  11Q GAIN WILD-TYPE                                                                                54
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11Q GAIN MUTATED                                                                                              4
  11Q GAIN WILD-TYPE                                                                                           73
D22V29, 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)                4
                                                                                              clus
vv                                                                                             11Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  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)                 73
[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"
D22V30, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  3
  11Q GAIN WILD-TYPE 52 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    3
  11Q GAIN WILD-TYPE   52   56
         clus
vv        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ABSENT                 2                 52
  PRESENT                3                 56
[1] 2 2
[1] FALSE
D22V31, continuous
D22V32, continuous
D22V33, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1  2
  11Q GAIN WILD-TYPE 34 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    2
  11Q GAIN WILD-TYPE   34   79
                                          clus
vv                                         11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    1                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                2                 79
[1] 2 2
[1] FALSE
D22V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  11Q GAIN MUTATED       0                    4                   0
  11Q GAIN WILD-TYPE     3                  109                   5
D22V35, multiclass
                      clus
vv                     11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY                4                109
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11Q GAIN MUTATED              2           1          0
  11Q GAIN WILD-TYPE            6          39         40
D22V36, multiclass
              clus
vv             11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CURRENT USER                2                  6
  FORMER USER                 1                 39
  NEVER USED                  0                 40
[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
D22V38, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    4  0
  11Q GAIN WILD-TYPE 69 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4    0
  11Q GAIN WILD-TYPE   69   14
         clus
vv        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ABSENT                 4                 69
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D22V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  11Q GAIN MUTATED     0    0   1    0    1  0   0    2    0   0   1  0  0
  11Q GAIN WILD-TYPE   2    1  21   51   20  3   6    4    8  13   1  1  7
D22V40, multiclass
      clus
vv     11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 1                 21
  T1B1                0                 51
  T1B2                1                 20
  T2                  0                  3
  T2A                 0                  6
  T2A1                2                  4
  T2A2                0                  8
  T2B                 0                 13
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V41, continuous

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    21   7
  12P GAIN WILD-TYPE 116  25
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                141 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 25 
$`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       182.93        25.35 
TCGA-C5-A7CK TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A439 
      134.33         9.34        13.61        22.98         0.76        14.50 
TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-FU-A3TX 
       13.91        14.96        23.84         2.17         1.45         1.48 
TCGA-FU-A5XV TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        1.97         5.42        29.72         0.07 

$`12P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        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-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MK TCGA-C5-A1MN 
       67.46        46.32        30.21        35.01         2.43        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
        3.58        44.22        73.45        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL 
        0.82        52.01        17.85        20.42       101.82        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
        9.67        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
        2.73        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QT 
      118.65        16.83        16.18         7.33         8.28        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       14.50         1.35         1.35         1.81        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
        0.26        14.89         1.48         0.69        14.99        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB 
        1.22         0.92         0.66         1.02         1.58         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        3.52         1.35         1.32         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         4.11       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       14.43        16.64        19.33        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
        5.13         0.10         0.89         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.03         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.07               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            182.93             177.04 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             20.50              12.59 
[1] "0.1 - 182.9 (20.5)" "0.0 - 177.0 (12.6)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 T1 T2+T3+T4
  12P GAIN MUTATED   16        6
  12P GAIN WILD-TYPE 81       33
D23V3, multiclass
          clus
vv         12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                     16                 81
  T2+T3+T4                6                 33
[1] 2 2
[1] FALSE
D23V4, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   16  5
  12P GAIN WILD-TYPE 71 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     16    5
  12P GAIN WILD-TYPE   71   35
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               16                 71
  1                5                 35
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12P GAIN MUTATED   12  0 10
  12P GAIN WILD-TYPE 60  3 55
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               12                 60
  M1                0                  3
  MX               10                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED               0                               25
  12P GAIN WILD-TYPE             2                              119
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12P GAIN MUTATED                                               0
  12P GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12P GAIN MUTATED                                     3
  12P GAIN WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12P GAIN MUTATED                                           0
  12P GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12P GAIN MUTATED                                              0
  12P GAIN WILD-TYPE                                            4
D23V6, multiclass
                                               clus
vv                                              12P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            25
  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                                              12P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             119
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     7  21
  12P GAIN WILD-TYPE  20 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7   21
  12P GAIN WILD-TYPE   20  128
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 7                 20
  YES               21                128
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     2
  12P GAIN WILD-TYPE                                7    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED                           2
  12P GAIN WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           0    22
  12P GAIN WILD-TYPE                                         1   108
D23V10, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    2                 13
  BLACK OR AFRICAN AMERICAN                                2                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   22                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"
D23V11, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1  21
  12P GAIN WILD-TYPE  10 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   21
  12P GAIN WILD-TYPE   10  106
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               21                106
[1] 2 2
[1] FALSE
D23V12, continuous
D23V13, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    9  4
  12P GAIN WILD-TYPE 39 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      9    4
  12P GAIN WILD-TYPE   39   15
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  TUMOR FREE                9                 39
  WITH TUMOR                4                 15
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  12P GAIN MUTATED         0      1       1            24       2
  12P GAIN WILD-TYPE       1      9       5           123      10
D23V14, multiclass
               clus
vv              12P GAIN MUTATED 12P GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      1                  5
  UNITED STATES               24                123
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  12P GAIN MUTATED    2 14 12  0  0
  12P GAIN WILD-TYPE 12 69 60  1  5
D23V15, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  G1                2                 12
  G2               14                 69
  G3               12                 60
  G4                0                  1
  GX                0                  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"
D23V16, continuous
D23V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  12P GAIN MUTATED                                             4
  12P GAIN WILD-TYPE                                          17
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  12P GAIN MUTATED                                        2
  12P GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  12P GAIN MUTATED                                                 1
  12P GAIN WILD-TYPE                                               0
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12P GAIN MUTATED                7                  13
  12P GAIN WILD-TYPE             29                  70
D23V18, multiclass
                                                 clus
vv                                                12P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 7
  LIFELONG NON-SMOKER                                           13
                                                 clus
vv                                                12P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  0
  CURRENT SMOKER                                                  29
  LIFELONG NON-SMOKER                                             70
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  12P GAIN MUTATED             5        6             2        0
  12P GAIN WILD-TYPE          12       31             9        5
D23V20, multiclass
               clus
vv              12P GAIN MUTATED 12P GAIN WILD-TYPE
  COMBINATION                  5                 12
  EXTERNAL                     6                 31
  EXTERNAL BEAM                2                  9
  INTERNAL                     0                  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"
D23V21, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  0
  12P GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    0
  12P GAIN WILD-TYPE   10    3
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D23V22, continuous
D23V23, continuous
D23V24, continuous
D23V25, continuous
D23V26, continuous
D23V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  12P GAIN MUTATED                                     0
  12P GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  12P GAIN MUTATED                                     1
  12P GAIN WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  12P GAIN MUTATED                         1                       0
  12P GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12P GAIN MUTATED                         2
  12P GAIN WILD-TYPE                       3
D23V28, multiclass
                                     clus
vv                                    12P GAIN MUTATED 12P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            1                  8
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  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)
  12P GAIN MUTATED                                               0
  12P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12P GAIN MUTATED                                                2
  12P GAIN WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12P GAIN MUTATED                                                                                  10
  12P GAIN WILD-TYPE                                                                                44
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12P GAIN MUTATED                                                                                              9
  12P GAIN WILD-TYPE                                                                                           68
D23V29, multiclass
                                                                                              clus
vv                                                                                             12P 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)                          10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                9
                                                                                              clus
vv                                                                                             12P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                8
  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)                 68
[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"
D23V30, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   11  8
  12P GAIN WILD-TYPE 43 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     11    8
  12P GAIN WILD-TYPE   43   51
         clus
vv        12P GAIN MUTATED 12P GAIN WILD-TYPE
  ABSENT                11                 43
  PRESENT                8                 51
[1] 2 2
[1] FALSE
D23V31, continuous
D23V32, continuous
D23V33, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   10 10
  12P GAIN WILD-TYPE 25 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     10   10
  12P GAIN WILD-TYPE   25   71
                                          clus
vv                                         12P GAIN MUTATED 12P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   10                 25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               10                 71
[1] 2 2
[1] FALSE
D23V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  12P GAIN MUTATED       0                   20                   0
  12P GAIN WILD-TYPE     3                   93                   5
D23V35, multiclass
                      clus
vv                     12P GAIN MUTATED 12P GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               20                 93
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12P GAIN MUTATED              1           7          4
  12P GAIN WILD-TYPE            7          33         36
D23V36, multiclass
              clus
vv             12P GAIN MUTATED 12P GAIN WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 7                 33
  NEVER USED                  4                 36
[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, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   10  3
  12P GAIN WILD-TYPE 63 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     10    3
  12P GAIN WILD-TYPE   63   11
         clus
vv        12P GAIN MUTATED 12P GAIN WILD-TYPE
  ABSENT                10                 63
  PRESENT                3                 11
[1] 2 2
[1] FALSE
D23V39, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  7 
        TCGA-C5-A1BN         TCGA-C5-A1MN         TCGA-C5-A1MP 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-MU-A51Y 
"12P GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  12P GAIN MUTATED     0    0   3    8    5  1   0    2    0   2   1  0  0
  12P GAIN WILD-TYPE   2    1  19   43   16  2   6    4    8  11   1  1  7
D23V40, multiclass
      clus
vv     12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 3                 19
  T1B1                8                 43
  T1B2                5                 16
  T2                  1                  2
  T2A                 0                  6
  T2A1                2                  4
  T2A2                0                  8
  T2B                 2                 11
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V41, continuous

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    19   6
  12Q GAIN WILD-TYPE 118  26
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                25                144 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 26 
$`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       182.93       134.33 
TCGA-C5-A7X3 TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A5ZF TCGA-FU-A23L 
        9.34        22.98         0.76        14.50        14.96        23.84 
TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A5XV TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        1.45         1.48         1.97         5.42        29.72         0.07 
TCGA-Q1-A5R3 
        5.85 

$`12Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        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-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MK 
       67.46        46.32        30.21        35.01        57.73         2.43 
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-A7CH TCGA-C5-A7CJ 
       38.43         0.82        17.85        20.42        25.35       101.82 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48         9.67        73.41        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       94.95        13.61         2.73        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       117.99       118.65        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       13.05         1.18        14.50         1.35         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         0.26        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
        0.69        14.99        13.58        13.48        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        6.64         0.53         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        0.36         1.18        23.70         2.24         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
       14.70         4.47         6.12         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        0.66         1.02         1.58         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.32         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU 
       19.33        20.48        15.58        10.06         5.13         0.10 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BF 
        0.89         0.07         0.82        13.87         0.03         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96         3.72         3.45         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            182.93             177.04 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             22.98              12.74 
[1] "0.1 - 182.9 (23.0)" "0.0 - 177.0 (12.7)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 T1 T2+T3+T4
  12Q GAIN MUTATED   14        5
  12Q GAIN WILD-TYPE 83       34
D24V3, multiclass
          clus
vv         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                     14                 83
  T2+T3+T4                5                 34
[1] 2 2
[1] FALSE
D24V4, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   13  5
  12Q GAIN WILD-TYPE 74 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     13    5
  12Q GAIN WILD-TYPE   74   35
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               13                 74
  1                5                 35
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED   10  0 10
  12Q GAIN WILD-TYPE 62  3 55
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               10                 62
  M1                0                  3
  MX               10                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED               0                               24
  12Q GAIN WILD-TYPE             2                              120
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12Q GAIN MUTATED                                               0
  12Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12Q GAIN MUTATED                                     1
  12Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12Q GAIN MUTATED                                           0
  12Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12Q GAIN MUTATED                                              0
  12Q GAIN WILD-TYPE                                            4
D24V6, multiclass
                                               clus
vv                                              12Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            24
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              12Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             120
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     7  18
  12Q GAIN WILD-TYPE  20 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7   18
  12Q GAIN WILD-TYPE   20  131
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 7                 20
  YES               18                131
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     2
  12Q GAIN WILD-TYPE                                7    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED                           1
  12Q GAIN WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           0    20
  12Q GAIN WILD-TYPE                                         1   110
D24V10, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    2                 13
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   20                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"
D24V11, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1  18
  12Q GAIN WILD-TYPE  10 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   18
  12Q GAIN WILD-TYPE   10  109
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               18                109
[1] 2 2
[1] FALSE
D24V12, continuous
D24V13, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8  4
  12Q GAIN WILD-TYPE 40 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8    4
  12Q GAIN WILD-TYPE   40   15
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  TUMOR FREE                8                 40
  WITH TUMOR                4                 15
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  12Q GAIN MUTATED         0      1       0            22       2
  12Q GAIN WILD-TYPE       1      9       6           125      10
D24V14, multiclass
               clus
vv              12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES               22                125
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  12Q GAIN MUTATED    1 13 11  0  0
  12Q GAIN WILD-TYPE 13 70 61  1  5
D24V15, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  G1                1                 13
  G2               13                 70
  G3               11                 61
  G4                0                  1
  GX                0                  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"
D24V16, continuous
D24V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  12Q GAIN MUTATED                                             4
  12Q GAIN WILD-TYPE                                          17
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  12Q GAIN MUTATED                                        2
  12Q GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  12Q GAIN MUTATED                                                 1
  12Q GAIN WILD-TYPE                                               0
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12Q GAIN MUTATED                6                  12
  12Q GAIN WILD-TYPE             30                  71
D24V18, multiclass
                                                 clus
vv                                                12Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                1
  CURRENT SMOKER                                                 6
  LIFELONG NON-SMOKER                                           12
                                                 clus
vv                                                12Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  0
  CURRENT SMOKER                                                  30
  LIFELONG NON-SMOKER                                             71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  12Q GAIN MUTATED             5        5             2        0
  12Q GAIN WILD-TYPE          12       32             9        5
D24V20, multiclass
               clus
vv              12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COMBINATION                  5                 12
  EXTERNAL                     5                 32
  EXTERNAL BEAM                2                  9
  INTERNAL                     0                  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"
D24V21, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  0
  12Q GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    0
  12Q GAIN WILD-TYPE   10    3
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D24V22, continuous
D24V23, continuous
D24V24, continuous
D24V25, continuous
D24V26, continuous
D24V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  12Q GAIN MUTATED                                     0
  12Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  12Q GAIN MUTATED                                     1
  12Q GAIN WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  12Q GAIN MUTATED                         1                       0
  12Q GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12Q GAIN MUTATED                         1
  12Q GAIN WILD-TYPE                       4
D24V28, multiclass
                                     clus
vv                                    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            1                  8
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  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)
  12Q GAIN MUTATED                                               0
  12Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12Q GAIN MUTATED                                                2
  12Q GAIN WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12Q GAIN MUTATED                                                                                  10
  12Q GAIN WILD-TYPE                                                                                44
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12Q GAIN MUTATED                                                                                              7
  12Q GAIN WILD-TYPE                                                                                           70
D24V29, multiclass
                                                                                              clus
vv                                                                                             12Q 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)                          10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                7
                                                                                              clus
vv                                                                                             12Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                8
  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)                 70
[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"
D24V30, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8  8
  12Q GAIN WILD-TYPE 46 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8    8
  12Q GAIN WILD-TYPE   46   51
         clus
vv        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ABSENT                 8                 46
  PRESENT                8                 51
[1] 2 2
[1] FALSE
D24V31, continuous
D24V32, continuous
D24V33, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8 10
  12Q GAIN WILD-TYPE 27 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8   10
  12Q GAIN WILD-TYPE   27   71
                                          clus
vv                                         12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    8                 27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               10                 71
[1] 2 2
[1] FALSE
D24V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  12Q GAIN MUTATED       0                   17                   0
  12Q GAIN WILD-TYPE     3                   96                   5
D24V35, multiclass
                      clus
vv                     12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               17                 96
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12Q GAIN MUTATED              1           7          3
  12Q GAIN WILD-TYPE            7          33         37
D24V36, multiclass
              clus
vv             12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 7                 33
  NEVER USED                  3                 37
[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, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    7  3
  12Q GAIN WILD-TYPE 66 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7    3
  12Q GAIN WILD-TYPE   66   11
         clus
vv        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ABSENT                 7                 66
  PRESENT                3                 11
[1] 2 2
[1] FALSE
D24V39, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                  7 
        TCGA-C5-A1BN         TCGA-C5-A1MN         TCGA-C5-A1MP 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-MU-A51Y 
"12Q GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  12Q GAIN MUTATED     0    0   3    7    4  1   0    2    0   1   1  0  1
  12Q GAIN WILD-TYPE   2    1  19   44   17  2   6    4    8  12   1  1  6
D24V40, multiclass
      clus
vv     12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 3                 19
  T1B1                7                 44
  T1B2                4                 17
  T2                  1                  2
  T2A                 0                  6
  T2A1                2                  4
  T2A2                0                  8
  T2B                 1                 12
  T3B                 1                  1
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V41, continuous

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    11   4
  13Q GAIN WILD-TYPE 126  28
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                154 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 28 
$`13Q GAIN MUTATED`
TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A2LZ TCGA-C5-A3HF TCGA-C5-A7X8 TCGA-EA-A3HT 
       35.01         0.46       100.14        17.85         2.73         0.62 
TCGA-EA-A3QD TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-FU-A40J 
       13.05        13.91        14.96         0.53         1.18         1.35 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A73R 
        0.07         2.96         6.25 

$`13Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-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-A2M1 
       44.22        73.18        73.45        83.05        78.35        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH 
        0.82        52.01        18.02        20.42       182.93        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48         9.67        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL 
       85.55        60.69        94.95         9.34        13.61        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18         7.33         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        1.74         1.32         0.82         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35        14.50         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
       14.89         1.48         0.69        14.99        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       12.59        45.96         6.64         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        0.03         0.36        23.70         2.24         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         4.47         6.12         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         3.52         1.32         1.97         1.12        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         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36        14.43        16.64        19.33        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       10.06         5.13         0.10         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-Q1-A5R1 
       13.87         0.03         5.42        29.72         4.34         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.45         5.85         3.39         3.72         5.75         4.80 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.07               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            100.14             182.93 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              2.96              14.15 
[1] "0.1 - 100.1 (3.0)"  "0.0 - 182.9 (14.1)"
[1] "hr=" "2.9"
D25V2, continuous
                    vv
clus                 T1 T2+T3+T4
  13Q GAIN MUTATED    7        4
  13Q GAIN WILD-TYPE 90       35
D25V3, multiclass
          clus
vv         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                      7                 90
  T2+T3+T4                4                 35
[1] 2 2
[1] FALSE
D25V4, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    6  4
  13Q GAIN WILD-TYPE 81 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6    4
  13Q GAIN WILD-TYPE   81   36
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                6                 81
  1                4                 36
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  13Q GAIN MUTATED    7  0  5
  13Q GAIN WILD-TYPE 65  3 60
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                7                 65
  M1                0                  3
  MX                5                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED               0                                9
  13Q GAIN WILD-TYPE             2                              135
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  13Q GAIN MUTATED                                               0
  13Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  13Q GAIN MUTATED                                     4
  13Q GAIN WILD-TYPE                                  16
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  13Q GAIN MUTATED                                           0
  13Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  13Q GAIN MUTATED                                              2
  13Q GAIN WILD-TYPE                                            2
D25V6, multiclass
                                               clus
vv                                              13Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             9
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              13Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             135
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   2
[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"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     2  13
  13Q GAIN WILD-TYPE  25 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   13
  13Q GAIN WILD-TYPE   25  136
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 2                 25
  YES               13                136
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     1
  13Q GAIN WILD-TYPE                                7    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED                           3
  13Q GAIN WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           0    11
  13Q GAIN WILD-TYPE                                         1   119
D25V10, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    1                 14
  BLACK OR AFRICAN AMERICAN                                3                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   11                119
[1] 5 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  12
  13Q GAIN WILD-TYPE  11 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   12
  13Q GAIN WILD-TYPE   11  115
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               12                115
[1] 2 2
[1] FALSE
D25V12, continuous
D25V13, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3  4
  13Q GAIN WILD-TYPE 45 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    4
  13Q GAIN WILD-TYPE   45   15
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  TUMOR FREE                3                 45
  WITH TUMOR                4                 15
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  13Q GAIN MUTATED         1      1       1            11       1
  13Q GAIN WILD-TYPE       0      9       5           136      11
D25V14, multiclass
               clus
vv              13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      1                  5
  UNITED STATES               11                136
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  13Q GAIN MUTATED    1  6  7  0  1
  13Q GAIN WILD-TYPE 13 77 65  1  4
D25V15, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  G1                1                 13
  G2                6                 77
  G3                7                 65
  G4                0                  1
  GX                1                  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"
D25V16, continuous
D25V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  13Q GAIN MUTATED                                             0
  13Q GAIN WILD-TYPE                                          21
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  13Q GAIN MUTATED                                        0
  13Q GAIN WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  13Q GAIN MUTATED                                                 0
  13Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  13Q GAIN MUTATED                3                   9
  13Q GAIN WILD-TYPE             33                  74
D25V18, multiclass
                                                 clus
vv                                                13Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 3
  LIFELONG NON-SMOKER                                            9
                                                 clus
vv                                                13Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  33
  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"
D25V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  13Q GAIN MUTATED             1        5             1        0
  13Q GAIN WILD-TYPE          16       32            10        5
D25V20, multiclass
               clus
vv              13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COMBINATION                  1                 16
  EXTERNAL                     5                 32
  EXTERNAL BEAM                1                 10
  INTERNAL                     0                  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"
D25V21, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    0  0
  13Q GAIN WILD-TYPE 11  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    0
  13Q GAIN WILD-TYPE   11    3
D25V22, continuous
D25V23, continuous
D25V24, continuous
D25V25, continuous
D25V26, continuous
D25V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  13Q GAIN MUTATED                                     0
  13Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  13Q GAIN MUTATED                                     0
  13Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  13Q GAIN MUTATED                         0                       0
  13Q GAIN WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  13Q GAIN MUTATED                         0
  13Q GAIN WILD-TYPE                       5
D25V28, multiclass
                    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                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  13Q GAIN MUTATED                                                                                   6
  13Q GAIN WILD-TYPE                                                                                48
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  13Q GAIN MUTATED                                                                                              6
  13Q GAIN WILD-TYPE                                                                                           71
D25V29, 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)                           6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                6
                                                                                              clus
vv                                                                                             13Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                9
  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)                 71
[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"
D25V30, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  6
  13Q GAIN WILD-TYPE 50 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    6
  13Q GAIN WILD-TYPE   50   53
         clus
vv        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ABSENT                 4                 50
  PRESENT                6                 53
[1] 2 2
[1] FALSE
D25V31, continuous
D25V32, continuous
D25V33, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2  5
  13Q GAIN WILD-TYPE 33 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    5
  13Q GAIN WILD-TYPE   33   76
                                          clus
vv                                         13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    2                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                5                 76
[1] 2 2
[1] FALSE
D25V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  13Q GAIN MUTATED       0                    9                   0
  13Q GAIN WILD-TYPE     3                  104                   5
D25V35, multiclass
                      clus
vv                     13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY                9                104
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  13Q GAIN MUTATED              0           4          2
  13Q GAIN WILD-TYPE            8          36         38
D25V36, multiclass
              clus
vv             13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CURRENT USER                0                  8
  FORMER USER                 4                 36
  NEVER USED                  2                 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"
D25V37, continuous
D25V38, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    6  0
  13Q GAIN WILD-TYPE 67 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6    0
  13Q GAIN WILD-TYPE   67   14
         clus
vv        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ABSENT                 6                 67
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D25V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  13Q GAIN MUTATED     0    0   1    4    2  0   1    1    0   1   1  0  1
  13Q GAIN WILD-TYPE   2    1  21   47   19  3   5    5    8  12   1  1  6
D25V40, multiclass
      clus
vv     13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 1                 21
  T1B1                4                 47
  T1B2                2                 19
  T2                  0                  3
  T2A                 1                  5
  T2A1                1                  5
  T2A2                0                  8
  T2B                 1                 12
  T3B                 1                  1
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V41, continuous

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    21   4
  14Q GAIN WILD-TYPE 116  28
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                25                144 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                 28 
$`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-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3QE 
       73.45        25.35         2.73         8.28         0.76         1.18 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2IP TCGA-EK-A2R7 
       14.50        14.89        13.91        14.96         6.64         0.59 
TCGA-EX-A3L1 TCGA-FU-A3HY TCGA-FU-A3NI TCGA-JW-A69B TCGA-LP-A5U3 TCGA-MY-A5BD 
        6.94         0.66         1.45        10.06         0.82        29.72 
TCGA-Q1-A6DT 
        3.39 

$`14Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        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-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ 
       46.32        30.21        35.01        57.73        53.16         0.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY 
        2.43        40.93         3.58        44.22        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         0.82        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       182.93       101.82       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       73.41        17.19        85.55        60.69        94.95         9.34 
TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       13.61        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QT 
      118.65        22.98        16.83        16.18         7.33        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 
        1.74         1.32         0.82         0.62        13.05        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
        1.48         0.69        14.99        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
       45.96         0.53         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        23.70         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.03        20.35         7.92        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
        6.12         1.22        23.84         0.92         2.17         1.02 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       19.33        20.48        15.58         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF 
        0.07        13.87         0.03         5.42         0.07         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96         3.72         3.45         5.85         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.59               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            173.29             182.93 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             13.91              13.53 
[1] "0.6 - 173.3 (13.9)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 T1 T2+T3+T4
  14Q GAIN MUTATED   16        5
  14Q GAIN WILD-TYPE 81       34
D26V3, multiclass
          clus
vv         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                     16                 81
  T2+T3+T4                5                 34
[1] 2 2
[1] FALSE
D26V4, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   11  8
  14Q GAIN WILD-TYPE 76 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     11    8
  14Q GAIN WILD-TYPE   76   32
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               11                 76
  1                8                 32
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  14Q GAIN MUTATED   15  0  7
  14Q GAIN WILD-TYPE 57  3 58
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0               15                 57
  M1                0                  3
  MX                7                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED               0                               23
  14Q GAIN WILD-TYPE             2                              121
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  14Q GAIN MUTATED                                               0
  14Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  14Q GAIN MUTATED                                     1
  14Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  14Q GAIN MUTATED                                           1
  14Q GAIN WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  14Q GAIN MUTATED                                              1
  14Q GAIN WILD-TYPE                                            3
D26V6, multiclass
                                               clus
vv                                              14Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            23
  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                                              14Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             121
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5  21
  14Q GAIN WILD-TYPE  22 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   21
  14Q GAIN WILD-TYPE   22  128
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 5                 22
  YES               21                128
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     3
  14Q GAIN WILD-TYPE                                7    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED                           1
  14Q GAIN WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           0    22
  14Q GAIN WILD-TYPE                                         1   108
D26V10, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    3                 12
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   22                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"
D26V11, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  21
  14Q GAIN WILD-TYPE   9 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   21
  14Q GAIN WILD-TYPE    9  106
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               21                106
[1] 2 2
[1] FALSE
D26V12, continuous
D26V13, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    7  5
  14Q GAIN WILD-TYPE 41 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      7    5
  14Q GAIN WILD-TYPE   41   14
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  TUMOR FREE                7                 41
  WITH TUMOR                5                 14
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  14Q GAIN MUTATED         0      3       1            19       3
  14Q GAIN WILD-TYPE       1      7       5           128       9
D26V14, multiclass
               clus
vv              14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       3                  7
  UKRAINE                      1                  5
  UNITED STATES               19                128
  VIETNAM                      3                  9
[1] 5 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                 G1 G2 G3 G4 GX
  14Q GAIN MUTATED    1 12 11  0  2
  14Q GAIN WILD-TYPE 13 71 61  1  3
D26V15, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  G1                1                 13
  G2               12                 71
  G3               11                 61
  G4                0                  1
  GX                2                  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"
D26V16, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 23 
        TCGA-BI-A0VR         TCGA-C5-A1BJ         TCGA-C5-A1BQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A2M2 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A7CM         TCGA-C5-A7CO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-EX-A69M         TCGA-FU-A2QG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-HM-A3JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LB 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-MU-A5YI         TCGA-MU-A8JM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D26V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  14Q GAIN MUTATED                                             1
  14Q GAIN WILD-TYPE                                          20
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  14Q GAIN MUTATED                                        1
  14Q GAIN WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  14Q GAIN MUTATED                                                 0
  14Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  14Q GAIN MUTATED                8                  13
  14Q GAIN WILD-TYPE             28                  70
D26V18, multiclass
                                                 clus
vv                                                14Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 8
  LIFELONG NON-SMOKER                                           13
                                                 clus
vv                                                14Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  28
  LIFELONG NON-SMOKER                                             70
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  14Q GAIN MUTATED             4        4             1        0
  14Q GAIN WILD-TYPE          13       33            10        5
D26V20, multiclass
               clus
vv              14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COMBINATION                  4                 13
  EXTERNAL                     4                 33
  EXTERNAL BEAM                1                 10
  INTERNAL                     0                  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"
D26V21, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    1  0
  14Q GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    0
  14Q GAIN WILD-TYPE   10    3
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D26V22, continuous
D26V23, continuous
D26V24, continuous
D26V25, continuous
D26V26, continuous
D26V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  14Q GAIN MUTATED                                     0
  14Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  14Q GAIN MUTATED                                     0
  14Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  14Q GAIN MUTATED                         0                       0
  14Q GAIN WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  14Q GAIN MUTATED                         0
  14Q GAIN WILD-TYPE                       5
D26V28, multiclass
                    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                                                2
  14Q GAIN WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  14Q GAIN MUTATED                                                                                   5
  14Q GAIN WILD-TYPE                                                                                49
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  14Q GAIN MUTATED                                                                                             15
  14Q GAIN WILD-TYPE                                                                                           62
D26V29, multiclass
                                                                                              clus
vv                                                                                             14Q 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)                           5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               15
                                                                                              clus
vv                                                                                             14Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 62
[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"
D26V30, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    9  9
  14Q GAIN WILD-TYPE 45 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      9    9
  14Q GAIN WILD-TYPE   45   50
         clus
vv        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ABSENT                 9                 45
  PRESENT                9                 50
[1] 2 2
[1] FALSE
D26V31, continuous
D26V32, continuous
D26V33, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    4 14
  14Q GAIN WILD-TYPE 31 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4   14
  14Q GAIN WILD-TYPE   31   67
                                          clus
vv                                         14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               14                 67
[1] 2 2
[1] FALSE
D26V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  14Q GAIN MUTATED       0                   17                   0
  14Q GAIN WILD-TYPE     3                   96                   5
D26V35, multiclass
                      clus
vv                     14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               17                 96
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  14Q GAIN MUTATED              3           3          9
  14Q GAIN WILD-TYPE            5          37         31
D26V36, multiclass
              clus
vv             14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  CURRENT USER                3                  5
  FORMER USER                 3                 37
  NEVER USED                  9                 31
[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, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   11  2
  14Q GAIN WILD-TYPE 62 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     11    2
  14Q GAIN WILD-TYPE   62   12
         clus
vv        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ABSENT                11                 62
  PRESENT                2                 12
[1] 2 2
[1] FALSE
D26V39, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                  8 
        TCGA-C5-A1BN         TCGA-C5-A1MN         TCGA-C5-A1MP 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  14Q GAIN MUTATED     1    0   4    8    3  0   1    2    1   1   0  0  1
  14Q GAIN WILD-TYPE   1    1  18   43   18  3   5    4    7  12   2  1  6
D26V40, multiclass
      clus
vv     14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1A                 1                  1
  T1A1                0                  1
  T1B                 4                 18
  T1B1                8                 43
  T1B2                3                 18
  T2                  0                  3
  T2A                 1                  5
  T2A1                2                  4
  T2A2                1                  7
  T2B                 1                 12
  T3B                 0                  2
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V41, continuous

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    21   8
  15Q GAIN WILD-TYPE 116  24
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                29                140 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 8                 24 
$`15Q GAIN MUTATED`
TCGA-BI-A0VR TCGA-C5-A1BF TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MI 
       49.48        18.74        31.40        30.21        57.73        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LZ TCGA-C5-A3HE 
        2.43        40.93         3.58        73.18       100.14        18.02 
TCGA-C5-A7CJ TCGA-C5-A7CM TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-EA-A3HQ TCGA-EA-A5O9 
      101.82         9.67         9.34         2.73         1.74        13.91 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RM TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L 
        4.04         0.03         2.24         6.94         4.47        23.84 
TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-LP-A4AU TCGA-MY-A5BE TCGA-R2-A69V 
       14.43        19.33         0.10         0.07        19.59 

$`15Q GAIN WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ 
       57.04        23.67        11.44        68.84        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A2LS 
       46.32        35.01        53.16        38.99         0.46        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         0.82        52.01 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42       182.93        25.35       134.33        15.48 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 
       73.41        17.19        85.55        60.69        94.95        13.61 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       12.36         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26        14.89         1.48         0.69        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.96        13.58        13.48        12.59        45.96         6.64 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.53         0.59         0.07         0.36         1.18        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92        14.70         6.12         1.22         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.66         1.02         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         1.12        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         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       36.36        16.64        20.48        15.58        10.06         5.13 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.89         0.07         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       29.72         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 
        3.39         3.72         5.75         4.80         6.25         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.03               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            101.82             182.93 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            14.430             13.265 
[1] "0.0 - 101.8 (14.4)" "0.0 - 182.9 (13.3)"
[1] "hr=" "1.8"
D27V2, continuous
                    vv
clus                 T1 T2+T3+T4
  15Q GAIN MUTATED   11        9
  15Q GAIN WILD-TYPE 86       30
D27V3, multiclass
          clus
vv         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                     11                 86
  T2+T3+T4                9                 30
[1] 2 2
[1] FALSE
D27V4, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   13  6
  15Q GAIN WILD-TYPE 74 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     13    6
  15Q GAIN WILD-TYPE   74   34
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               13                 74
  1                6                 34
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  15Q GAIN MUTATED   12  0  9
  15Q GAIN WILD-TYPE 60  3 56
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               12                 60
  M1                0                  3
  MX                9                 56
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED               0                               26
  15Q GAIN WILD-TYPE             2                              118
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  15Q GAIN MUTATED                                               1
  15Q GAIN WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  15Q GAIN MUTATED                                     2
  15Q GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  15Q GAIN MUTATED                                           0
  15Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  15Q GAIN MUTATED                                              1
  15Q GAIN WILD-TYPE                                            3
D27V6, multiclass
                                               clus
vv                                              15Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            26
  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                                              15Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             118
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     7  23
  15Q GAIN WILD-TYPE  20 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7   23
  15Q GAIN WILD-TYPE   20  126
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 7                 20
  YES               23                126
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  3     2
  15Q GAIN WILD-TYPE                                4    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED                           2
  15Q GAIN WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           0    22
  15Q GAIN WILD-TYPE                                         1   108
D27V10, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  4
  ASIAN                                                    2                 13
  BLACK OR AFRICAN AMERICAN                                2                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   22                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"
D27V11, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     4  22
  15Q GAIN WILD-TYPE   7 105
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4   22
  15Q GAIN WILD-TYPE    7  105
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               22                105
[1] 2 2
[1] FALSE
D27V12, continuous
D27V13, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    7  6
  15Q GAIN WILD-TYPE 41 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7    6
  15Q GAIN WILD-TYPE   41   13
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  TUMOR FREE                7                 41
  WITH TUMOR                6                 13
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  15Q GAIN MUTATED         0      1       1            27       1
  15Q GAIN WILD-TYPE       1      9       5           120      11
D27V14, multiclass
               clus
vv              15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      1                  5
  UNITED STATES               27                120
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  15Q GAIN MUTATED    2 12 16  0  0
  15Q GAIN WILD-TYPE 12 71 56  1  5
D27V15, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  G1                2                 12
  G2               12                 71
  G3               16                 56
  G4                0                  1
  GX                0                  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"
D27V16, continuous
D27V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  15Q GAIN MUTATED                                             3
  15Q GAIN WILD-TYPE                                          18
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  15Q GAIN MUTATED                                        0
  15Q GAIN WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  15Q GAIN MUTATED                                                 0
  15Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  15Q GAIN MUTATED                7                  17
  15Q GAIN WILD-TYPE             29                  66
D27V18, multiclass
                                                 clus
vv                                                15Q GAIN 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                                                 7
  LIFELONG NON-SMOKER                                           17
                                                 clus
vv                                                15Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  29
  LIFELONG NON-SMOKER                                             66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  15Q GAIN MUTATED             5       10             2        0
  15Q GAIN WILD-TYPE          12       27             9        5
D27V20, multiclass
               clus
vv              15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COMBINATION                  5                 12
  EXTERNAL                    10                 27
  EXTERNAL BEAM                2                  9
  INTERNAL                     0                  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"
D27V21, binary
                    cls
clus                 0 1
  15Q GAIN MUTATED   4 1
  15Q GAIN WILD-TYPE 7 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4    1
  15Q GAIN WILD-TYPE    7    2
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CGY                4                  7
  GY                 1                  2
[1] 2 2
[1] FALSE
D27V22, continuous
D27V23, continuous
D27V24, continuous
D27V25, continuous
D27V26, continuous
D27V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  15Q GAIN MUTATED                                     0
  15Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  15Q GAIN MUTATED                                     0
  15Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  15Q GAIN MUTATED                         0                       0
  15Q GAIN WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  15Q GAIN MUTATED                         0
  15Q GAIN WILD-TYPE                       5
D27V28, multiclass
                    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                                                2
  15Q GAIN WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  15Q GAIN MUTATED                                                                                  10
  15Q GAIN WILD-TYPE                                                                                44
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  15Q GAIN MUTATED                                                                                              9
  15Q GAIN WILD-TYPE                                                                                           68
D27V29, multiclass
                                                                                              clus
vv                                                                                             15Q 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)                          10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                9
                                                                                              clus
vv                                                                                             15Q GAIN WILD-TYPE
  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)                            44
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 68
[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"
D27V30, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    9  8
  15Q GAIN WILD-TYPE 45 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9    8
  15Q GAIN WILD-TYPE   45   51
         clus
vv        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ABSENT                 9                 45
  PRESENT                8                 51
[1] 2 2
[1] FALSE
D27V31, continuous
D27V32, continuous
D27V33, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6 11
  15Q GAIN WILD-TYPE 29 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6   11
  15Q GAIN WILD-TYPE   29   70
                                          clus
vv                                         15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               11                 70
[1] 2 2
[1] FALSE
D27V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  15Q GAIN MUTATED       0                   16                   1
  15Q GAIN WILD-TYPE     3                   97                   4
D27V35, multiclass
                      clus
vv                     15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               16                 97
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  15Q GAIN MUTATED              2           3          7
  15Q GAIN WILD-TYPE            6          37         33
D27V36, multiclass
              clus
vv             15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CURRENT USER                2                  6
  FORMER USER                 3                 37
  NEVER USED                  7                 33
[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
D27V38, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    9  2
  15Q GAIN WILD-TYPE 64 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9    2
  15Q GAIN WILD-TYPE   64   12
         clus
vv        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ABSENT                 9                 64
  PRESENT                2                 12
[1] 2 2
[1] FALSE
D27V39, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                  7 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-EK-A2RO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-MU-A51Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM 
"15Q GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  15Q GAIN MUTATED     0    0   3    5    3  1   4    2    0   2   0  0  1
  15Q GAIN WILD-TYPE   2    1  19   46   18  2   2    4    8  11   2  1  6
D27V40, multiclass
      clus
vv     15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 3                 19
  T1B1                5                 46
  T1B2                3                 18
  T2                  1                  2
  T2A                 4                  2
  T2A1                2                  4
  T2A2                0                  8
  T2B                 2                 11
  T3B                 0                  2
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V41, continuous

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    20   4
  16P GAIN WILD-TYPE 117  28
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                24                145 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 28 
$`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-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3QD 
       25.35         2.73        22.98         8.28         1.74        13.05 
TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2RD TCGA-EK-A2RL TCGA-EX-A69L 
       14.50        13.91        14.96         0.03        23.70         4.47 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A40J TCGA-JW-A5VJ TCGA-PN-A8MA TCGA-UC-A7PF 
       23.84         1.45         1.35        19.33         2.96        93.99 

$`16P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        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-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ 
       67.46        30.21        35.01        57.73        53.16         0.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
        2.43        40.93         3.58        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         0.82        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       182.93       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
        9.67        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        9.34        13.61        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS 
      117.99       118.65        16.83        16.18         7.33         0.76 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 
       12.36         1.32         0.82         0.62         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
       14.89         1.48         0.69        14.99        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB 
       12.59        45.96         6.64         0.53         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        4.04         0.36         1.18         2.24         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       14.70         6.12         1.22         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        1.02         1.58         1.48         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.07         4.34         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD 
       11.67 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.03               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             93.99             182.93 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            17.145             12.660 
[1] "0.0 - 94.0 (17.1)"  "0.0 - 182.9 (12.7)"
[1] "hr=" "1"  
D28V2, continuous
                    vv
clus                 T1 T2+T3+T4
  16P GAIN MUTATED   12        9
  16P GAIN WILD-TYPE 85       30
D28V3, multiclass
          clus
vv         16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                     12                 85
  T2+T3+T4                9                 30
[1] 2 2
[1] FALSE
D28V4, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   10  9
  16P GAIN WILD-TYPE 77 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     10    9
  16P GAIN WILD-TYPE   77   31
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               10                 77
  1                9                 31
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16P GAIN MUTATED   13  0  8
  16P GAIN WILD-TYPE 59  3 57
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               13                 59
  M1                0                  3
  MX                8                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED               0                               20
  16P GAIN WILD-TYPE             2                              124
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16P GAIN MUTATED                                               1
  16P GAIN WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16P GAIN MUTATED                                     2
  16P GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16P GAIN MUTATED                                           0
  16P GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16P GAIN MUTATED                                              1
  16P GAIN WILD-TYPE                                            3
D28V6, multiclass
                                               clus
vv                                              16P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            20
  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                                              16P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             124
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     4  20
  16P GAIN WILD-TYPE  23 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4   20
  16P GAIN WILD-TYPE   23  129
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                 23
  YES               20                129
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  2     3
  16P GAIN WILD-TYPE                                5    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED                           2
  16P GAIN WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           0    15
  16P GAIN WILD-TYPE                                         1   115
D28V10, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  5
  ASIAN                                                    3                 12
  BLACK OR AFRICAN AMERICAN                                2                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                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"
D28V11, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  19
  16P GAIN WILD-TYPE  10 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   19
  16P GAIN WILD-TYPE   10  108
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               19                108
[1] 2 2
[1] FALSE
D28V12, continuous
D28V13, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    6  6
  16P GAIN WILD-TYPE 42 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6    6
  16P GAIN WILD-TYPE   42   13
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  TUMOR FREE                6                 42
  WITH TUMOR                6                 13
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  16P GAIN MUTATED         1      1       1            19       2
  16P GAIN WILD-TYPE       0      9       5           128      10
D28V14, multiclass
               clus
vv              16P GAIN MUTATED 16P GAIN WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      1                  5
  UNITED STATES               19                128
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  16P GAIN MUTATED    1 12 11  0  0
  16P GAIN WILD-TYPE 13 71 61  1  5
D28V15, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  G1                1                 13
  G2               12                 71
  G3               11                 61
  G4                0                  1
  GX                0                  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"
D28V16, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 23 
        TCGA-BI-A0VR         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1ME         TCGA-C5-A1MF 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A7CM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-EX-A69M         TCGA-FU-A2QG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-HM-A3JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-MU-A5YI         TCGA-MU-A8JM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
D28V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16P GAIN MUTATED                                             0
  16P GAIN WILD-TYPE                                          21
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  16P GAIN MUTATED                                        2
  16P GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  16P GAIN MUTATED                                                 0
  16P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16P GAIN MUTATED                7                  12
  16P GAIN WILD-TYPE             29                  71
D28V18, multiclass
                                                 clus
vv                                                16P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 7
  LIFELONG NON-SMOKER                                           12
                                                 clus
vv                                                16P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  29
  LIFELONG NON-SMOKER                                             71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  16P GAIN MUTATED             3        6             1        0
  16P GAIN WILD-TYPE          14       31            10        5
D28V20, multiclass
               clus
vv              16P GAIN MUTATED 16P GAIN WILD-TYPE
  COMBINATION                  3                 14
  EXTERNAL                     6                 31
  EXTERNAL BEAM                1                 10
  INTERNAL                     0                  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"
D28V21, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    1  0
  16P GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    0
  16P GAIN WILD-TYPE   10    3
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D28V22, continuous
D28V23, continuous
D28V24, continuous
D28V25, continuous
D28V26, continuous
D28V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  16P GAIN MUTATED                                     0
  16P GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  16P GAIN MUTATED                                     0
  16P GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  16P GAIN MUTATED                         1                       0
  16P GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16P GAIN MUTATED                         0
  16P GAIN WILD-TYPE                       5
D28V28, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 22 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A2LX         TCGA-DR-A0ZM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-EA-A50E         TCGA-EK-A2RN 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-EX-A1H5         TCGA-EX-A449 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-HM-A4S6         TCGA-IR-A3LH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-MU-A8JM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-UC-A7PD 
"16P GAIN WILD-TYPE" 
                    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                                                2
  16P GAIN WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16P GAIN MUTATED                                                                                   7
  16P GAIN WILD-TYPE                                                                                47
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16P GAIN MUTATED                                                                                             11
  16P GAIN WILD-TYPE                                                                                           66
D28V29, multiclass
                                                                                              clus
vv                                                                                             16P 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)               11
                                                                                              clus
vv                                                                                             16P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                8
  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)                 66
[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"
D28V30, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    8  9
  16P GAIN WILD-TYPE 46 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      8    9
  16P GAIN WILD-TYPE   46   50
         clus
vv        16P GAIN MUTATED 16P GAIN WILD-TYPE
  ABSENT                 8                 46
  PRESENT                9                 50
[1] 2 2
[1] FALSE
D28V31, continuous
D28V32, continuous
D28V33, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3 13
  16P GAIN WILD-TYPE 32 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   13
  16P GAIN WILD-TYPE   32   68
                                          clus
vv                                         16P GAIN MUTATED 16P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               13                 68
[1] 2 2
[1] FALSE
D28V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  16P GAIN MUTATED       0                   18                   0
  16P GAIN WILD-TYPE     3                   95                   5
D28V35, multiclass
                      clus
vv                     16P GAIN MUTATED 16P GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               18                 95
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16P GAIN MUTATED              0           5          6
  16P GAIN WILD-TYPE            8          35         34
D28V36, multiclass
              clus
vv             16P GAIN MUTATED 16P GAIN WILD-TYPE
  CURRENT USER                0                  8
  FORMER USER                 5                 35
  NEVER USED                  6                 34
[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
D28V38, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    6  4
  16P GAIN WILD-TYPE 67 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6    4
  16P GAIN WILD-TYPE   67   10
         clus
vv        16P GAIN MUTATED 16P GAIN WILD-TYPE
  ABSENT                 6                 67
  PRESENT                4                 10
[1] 2 2
[1] FALSE
D28V39, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                  8 
        TCGA-C5-A1BN         TCGA-C5-A1MN         TCGA-C5-A1MP 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  16P GAIN MUTATED     0    0   1    9    2  0   2    3    1   2   1  0  0
  16P GAIN WILD-TYPE   2    1  21   42   19  3   4    3    7  11   1  1  7
D28V40, multiclass
      clus
vv     16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 1                 21
  T1B1                9                 42
  T1B2                2                 19
  T2                  0                  3
  T2A                 2                  4
  T2A1                3                  3
  T2A2                1                  7
  T2B                 2                 11
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V41, continuous

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    15   6
  16Q GAIN WILD-TYPE 122  26
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                21                148 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 26 
$`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        25.35 
TCGA-C5-A7UC TCGA-C5-A7X8 TCGA-DS-A3LQ TCGA-DS-A7WI TCGA-EA-A3QD TCGA-EA-A439 
       17.19         2.73        22.98         8.28        13.05        14.50 
TCGA-EA-A5ZF TCGA-EK-A2RM TCGA-EX-A3L1 TCGA-EX-A69L TCGA-FU-A23L TCGA-FU-A40J 
       14.96         2.24         6.94         4.47        23.84         1.35 
TCGA-JW-A5VJ TCGA-PN-A8MA TCGA-UC-A7PD 
       19.33         2.96        11.67 

$`16Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        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-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ 
       67.46        30.21        35.01        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-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43         0.82        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       182.93       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48         9.67        73.41        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        9.34        13.61        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS 
      117.99       118.65        16.83        16.18         7.33         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
       12.36         1.74         1.32         0.82         0.62         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       14.50         1.35         1.35         1.81        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        0.26        14.89         1.48        13.91         0.69        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.58        13.48        12.59        45.96         6.64         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.59         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       23.70         0.10         0.07         0.10         0.10         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         6.12         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         3.52         1.32         1.97         1.12        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         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       36.36        14.43        16.64        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
        5.13         0.10         0.89         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 
        0.03         5.42        29.72         0.07         4.34         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.45         5.85         3.39         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        6.25        19.59         3.88        93.99 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              1.35               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             57.04             182.93 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             14.96              13.15 
[1] "1.4 - 57.0 (15.0)"  "0.0 - 182.9 (13.2)"
[1] "hr=" "2.3"
D29V2, continuous
                    vv
clus                 T1 T2+T3+T4
  16Q GAIN MUTATED    8        9
  16Q GAIN WILD-TYPE 89       30
D29V3, multiclass
          clus
vv         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                      8                 89
  T2+T3+T4                9                 30
[1] 2 2
[1] FALSE
D29V4, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    9  6
  16Q GAIN WILD-TYPE 78 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      9    6
  16Q GAIN WILD-TYPE   78   34
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                9                 78
  1                6                 34
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16Q GAIN MUTATED   12  0  5
  16Q GAIN WILD-TYPE 60  3 60
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               12                 60
  M1                0                  3
  MX                5                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED               0                               19
  16Q GAIN WILD-TYPE             2                              125
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16Q GAIN MUTATED                                               0
  16Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16Q GAIN MUTATED                                     1
  16Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16Q GAIN MUTATED                                           0
  16Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16Q GAIN MUTATED                                              1
  16Q GAIN WILD-TYPE                                            3
D29V6, multiclass
                                               clus
vv                                              16Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            19
  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                                              16Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             125
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     4  17
  16Q GAIN WILD-TYPE  23 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4   17
  16Q GAIN WILD-TYPE   23  132
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 4                 23
  YES               17                132
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  2     3
  16Q GAIN WILD-TYPE                                5    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED                           1
  16Q GAIN WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           0    14
  16Q GAIN WILD-TYPE                                         1   116
D29V10, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  5
  ASIAN                                                    3                 12
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                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"
D29V11, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  15
  16Q GAIN WILD-TYPE  10 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   15
  16Q GAIN WILD-TYPE   10  112
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               15                112
[1] 2 2
[1] FALSE
D29V12, continuous
D29V13, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    5  6
  16Q GAIN WILD-TYPE 43 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5    6
  16Q GAIN WILD-TYPE   43   13
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  TUMOR FREE                5                 43
  WITH TUMOR                6                 13
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  16Q GAIN MUTATED         1      0       0            18       2
  16Q GAIN WILD-TYPE       0     10       6           129      10
D29V14, multiclass
               clus
vv              16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       0                 10
  UKRAINE                      0                  6
  UNITED STATES               18                129
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  16Q GAIN MUTATED    0  7 14  0  0
  16Q GAIN WILD-TYPE 14 76 58  1  5
D29V15, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  G1                0                 14
  G2                7                 76
  G3               14                 58
  G4                0                  1
  GX                0                  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"
D29V16, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 23 
        TCGA-BI-A0VR         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1ME         TCGA-C5-A1MF 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A7CM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-EX-A69M         TCGA-FU-A2QG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-MU-A5YI         TCGA-MU-A8JM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D29V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16Q GAIN MUTATED                                             0
  16Q GAIN WILD-TYPE                                          21
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  16Q GAIN MUTATED                                        2
  16Q GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  16Q GAIN MUTATED                                                 0
  16Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16Q GAIN MUTATED                5                  11
  16Q GAIN WILD-TYPE             31                  72
D29V18, multiclass
                                                 clus
vv                                                16Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 5
  LIFELONG NON-SMOKER                                           11
                                                 clus
vv                                                16Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  31
  LIFELONG NON-SMOKER                                             72
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  16Q GAIN MUTATED             3        6             1        1
  16Q GAIN WILD-TYPE          14       31            10        4
D29V20, multiclass
               clus
vv              16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COMBINATION                  3                 14
  EXTERNAL                     6                 31
  EXTERNAL BEAM                1                 10
  INTERNAL                     1                  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"
D29V21, binary
                    cls
clus                 0 1
  16Q GAIN MUTATED   2 0
  16Q GAIN WILD-TYPE 9 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    0
  16Q GAIN WILD-TYPE    9    3
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CGY                2                  9
  GY                 0                  3
[1] 2 2
[1] FALSE
D29V22, continuous
D29V23, continuous
D29V24, continuous
D29V25, continuous
D29V26, continuous
D29V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  16Q GAIN MUTATED                                     0
  16Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  16Q GAIN MUTATED                                     0
  16Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  16Q GAIN MUTATED                         2                       0
  16Q GAIN WILD-TYPE                       7                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16Q GAIN MUTATED                         0
  16Q GAIN WILD-TYPE                       5
D29V28, multiclass
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 21 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A2LX         TCGA-DR-A0ZM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-EA-A50E         TCGA-EK-A2RN 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-EX-A1H5         TCGA-EX-A449 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-HM-A4S6         TCGA-IR-A3LH 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-MU-A8JM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
                    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                                                2
  16Q GAIN WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16Q GAIN MUTATED                                                                                   5
  16Q GAIN WILD-TYPE                                                                                49
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16Q GAIN MUTATED                                                                                             10
  16Q GAIN WILD-TYPE                                                                                           67
D29V29, multiclass
                                                                                              clus
vv                                                                                             16Q 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)                           5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               10
                                                                                              clus
vv                                                                                             16Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            49
  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"
D29V30, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    5  9
  16Q GAIN WILD-TYPE 49 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5    9
  16Q GAIN WILD-TYPE   49   50
         clus
vv        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ABSENT                 5                 49
  PRESENT                9                 50
[1] 2 2
[1] FALSE
D29V31, continuous
D29V32, continuous
D29V33, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3 12
  16Q GAIN WILD-TYPE 32 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   12
  16Q GAIN WILD-TYPE   32   69
                                          clus
vv                                         16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               12                 69
[1] 2 2
[1] FALSE
D29V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  16Q GAIN MUTATED       0                   14                   0
  16Q GAIN WILD-TYPE     3                   99                   5
D29V35, multiclass
                      clus
vv                     16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               14                 99
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16Q GAIN MUTATED              1           6          4
  16Q GAIN WILD-TYPE            7          34         36
D29V36, multiclass
              clus
vv             16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 6                 34
  NEVER USED                  4                 36
[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
D29V38, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    5  2
  16Q GAIN WILD-TYPE 68 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5    2
  16Q GAIN WILD-TYPE   68   12
         clus
vv        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ABSENT                 5                 68
  PRESENT                2                 12
[1] 2 2
[1] FALSE
D29V39, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  8 
        TCGA-C5-A1BN         TCGA-C5-A1MN         TCGA-C5-A1MP 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  16Q GAIN MUTATED     0    0   3    5    0  0   1    4    1   2   1  0  0
  16Q GAIN WILD-TYPE   2    1  19   46   21  3   5    2    7  11   1  1  7
D29V40, multiclass
      clus
vv     16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 3                 19
  T1B1                5                 46
  T1B2                0                 21
  T2                  0                  3
  T2A                 1                  5
  T2A1                4                  2
  T2A2                1                  7
  T2B                 2                 11
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V41, continuous

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED     8   3
  17P GAIN WILD-TYPE 129  29
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                158 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 29 
$`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        25.35        85.55 
TCGA-DS-A3LQ TCGA-EA-A3HR TCGA-FU-A40J TCGA-Q1-A5R3 TCGA-UC-A7PF 
       22.98         1.32         1.35         5.85        93.99 

$`17P 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-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-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       67.46        46.32        30.21        57.73        53.16        38.99 
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         0.82 
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       182.93       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
      134.33        15.48         9.67        73.41        17.19        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       94.95         9.34        13.61         2.73        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       117.99       118.65        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS 
        7.33         8.28         0.76        12.36         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50         1.81        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        2.24         0.10         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17         0.66         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        1.45         1.58         1.48         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU 
       19.33        20.48        15.58        10.06         5.13         0.10 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.89         0.07         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       29.72         0.07         4.34         2.96         3.72         3.45 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD 
        3.88        11.67 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.32               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             93.99             182.93 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            25.350             12.935 
[1] "1.3 - 94.0 (25.4)"  "0.0 - 182.9 (12.9)"
[1] "hr=" "1.2"
D30V2, continuous
                    vv
clus                 T1 T2+T3+T4
  17P GAIN MUTATED    3        4
  17P GAIN WILD-TYPE 94       35
D30V3, multiclass
          clus
vv         17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                      3                 94
  T2+T3+T4                4                 35
[1] 2 2
[1] FALSE
D30V4, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    2  5
  17P GAIN WILD-TYPE 85 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    5
  17P GAIN WILD-TYPE   85   35
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                2                 85
  1                5                 35
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17P GAIN MUTATED    6  0  2
  17P GAIN WILD-TYPE 66  3 63
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                6                 66
  M1                0                  3
  MX                2                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED               0                               10
  17P GAIN WILD-TYPE             2                              134
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17P GAIN MUTATED                                               0
  17P GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17P GAIN MUTATED                                     2
  17P GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17P GAIN MUTATED                                           0
  17P GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17P GAIN MUTATED                                              0
  17P GAIN WILD-TYPE                                            4
D30V6, multiclass
                                               clus
vv                                              17P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            10
  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                                              17P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             134
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4   8
  17P GAIN WILD-TYPE  23 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    8
  17P GAIN WILD-TYPE   23  141
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 4                 23
  YES                8                141
[1] 2 2
[1] FALSE
D30V8, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 51 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LZ         TCGA-C5-A2M2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7UI         TCGA-C5-A7X8         TCGA-DR-A0ZM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-EA-A556 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JW-A5VI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-MU-A5YI         TCGA-MU-A8JM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741         TCGA-UC-A7PD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D30V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     0
  17P GAIN WILD-TYPE                                7    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED                           0
  17P GAIN WILD-TYPE                        18
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0    10
  17P GAIN WILD-TYPE                                         1   120
D30V10, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    0                 15
  BLACK OR AFRICAN AMERICAN                                0                 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   10                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"
D30V11, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0   7
  17P GAIN WILD-TYPE  11 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    7
  17P GAIN WILD-TYPE   11  120
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                7                120
[1] 2 2
[1] FALSE
D30V12, continuous
D30V13, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    1  3
  17P GAIN WILD-TYPE 47 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    3
  17P GAIN WILD-TYPE   47   16
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  TUMOR FREE                1                 47
  WITH TUMOR                3                 16
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  17P GAIN MUTATED         0      1       0            11       0
  17P GAIN WILD-TYPE       1      9       6           136      12
D30V14, multiclass
               clus
vv              17P GAIN MUTATED 17P GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES               11                136
  VIETNAM                      0                 12
[1] 5 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                 G1 G2 G3 G4 GX
  17P GAIN MUTATED    0  6  6  0  0
  17P GAIN WILD-TYPE 14 77 66  1  5
D30V15, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  G1                0                 14
  G2                6                 77
  G3                6                 66
  G4                0                  1
  GX                0                  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"
D30V16, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 24 
        TCGA-BI-A0VR         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1ME         TCGA-C5-A1MF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A2M2         TCGA-C5-A3HD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7CM         TCGA-C5-A7CO         TCGA-EX-A69M 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3TX         TCGA-FU-A3WB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-HM-A4S6         TCGA-IR-A3L7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-MU-A5YI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D30V17, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 51 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LZ         TCGA-C5-A2M2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7UI         TCGA-C5-A7X8         TCGA-DR-A0ZM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-EA-A556 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JW-A5VI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-MU-A5YI         TCGA-MU-A8JM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741         TCGA-UC-A7PD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17P GAIN MUTATED                                             0
  17P GAIN WILD-TYPE                                          21
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  17P GAIN MUTATED                                        1
  17P GAIN WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  17P GAIN MUTATED                                                 0
  17P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17P GAIN MUTATED                3                   6
  17P GAIN WILD-TYPE             33                  77
D30V18, multiclass
                                                 clus
vv                                                17P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 3
  LIFELONG NON-SMOKER                                            6
                                                 clus
vv                                                17P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  33
  LIFELONG NON-SMOKER                                             77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V19, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 46 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LZ         TCGA-C5-A2M2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7X8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-EA-A556 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3TX 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-HM-A4S6         TCGA-HM-A6W2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VK         TCGA-MU-A5YI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-UC-A7PD 
"17P GAIN WILD-TYPE" 
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  17P GAIN MUTATED             2        2             2        0
  17P GAIN WILD-TYPE          15       35             9        5
D30V20, multiclass
               clus
vv              17P GAIN MUTATED 17P GAIN WILD-TYPE
  COMBINATION                  2                 15
  EXTERNAL                     2                 35
  EXTERNAL BEAM                2                  9
  INTERNAL                     0                  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"
D30V21, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    0  0
  17P GAIN WILD-TYPE 11  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    0
  17P GAIN WILD-TYPE   11    3
D30V22, continuous
D30V23, continuous
D30V24, continuous
D30V25, continuous
D30V26, continuous
D30V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  17P GAIN MUTATED                                     0
  17P GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  17P GAIN MUTATED                                     1
  17P GAIN WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  17P GAIN MUTATED                         1                       0
  17P GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17P GAIN MUTATED                         0
  17P GAIN WILD-TYPE                       5
D30V28, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 21 
        TCGA-C5-A0TN         TCGA-C5-A1BE         TCGA-C5-A1BM 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-DR-A0ZM         TCGA-DS-A0VK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EK-A2RN         TCGA-EK-A2RO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A8JM         TCGA-UC-A7PD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
                    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                                                1
  17P GAIN WILD-TYPE                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17P GAIN MUTATED                                                                                   4
  17P GAIN WILD-TYPE                                                                                50
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17P GAIN MUTATED                                                                                              4
  17P GAIN WILD-TYPE                                                                                           73
D30V29, multiclass
                                                                                              clus
vv                                                                                             17P 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)                           4
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                4
                                                                                              clus
vv                                                                                             17P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            50
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 73
[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"
D30V30, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    1  6
  17P GAIN WILD-TYPE 53 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    6
  17P GAIN WILD-TYPE   53   53
         clus
vv        17P GAIN MUTATED 17P GAIN WILD-TYPE
  ABSENT                 1                 53
  PRESENT                6                 53
[1] 2 2
[1] FALSE
D30V31, continuous
D30V32, continuous
D30V33, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    2  4
  17P GAIN WILD-TYPE 33 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    4
  17P GAIN WILD-TYPE   33   77
                                          clus
vv                                         17P GAIN MUTATED 17P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    2                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                4                 77
[1] 2 2
[1] FALSE
D30V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  17P GAIN MUTATED       0                    7                   0
  17P GAIN WILD-TYPE     3                  106                   5
D30V35, multiclass
                      clus
vv                     17P GAIN MUTATED 17P GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY                7                106
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17P GAIN MUTATED              0           4          1
  17P GAIN WILD-TYPE            8          36         39
D30V36, multiclass
              clus
vv             17P GAIN MUTATED 17P GAIN WILD-TYPE
  CURRENT USER                0                  8
  FORMER USER                 4                 36
  NEVER USED                  1                 39
[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
D30V38, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    4  2
  17P GAIN WILD-TYPE 69 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    2
  17P GAIN WILD-TYPE   69   12
         clus
vv        17P GAIN MUTATED 17P GAIN WILD-TYPE
  ABSENT                 4                 69
  PRESENT                2                 12
[1] 2 2
[1] FALSE
D30V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  17P GAIN MUTATED     0    0   0    3    0  0   1    1    0   0   2  0  1
  17P GAIN WILD-TYPE   2    1  22   48   21  3   5    5    8  13   0  1  6
D30V40, multiclass
      clus
vv     17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 0                 22
  T1B1                3                 48
  T1B2                0                 21
  T2                  0                  3
  T2A                 1                  5
  T2A1                1                  5
  T2A2                0                  8
  T2B                 0                 13
  T3B                 2                  0
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V41, continuous

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    19   5
  17Q GAIN WILD-TYPE 118  27
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                24                145 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 27 
$`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-DS-A3LQ TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A439 
       25.35        85.55        22.98         1.32        13.05        14.50 
TCGA-EA-A5ZF TCGA-EK-A2RM TCGA-EK-A3GK TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A40J 
       14.96         2.24         0.10         6.94         6.12         1.35 
TCGA-JW-A69B TCGA-LP-A4AU TCGA-MU-A51Y TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-UC-A7PF 
       10.06         0.10        13.87         3.45         5.85        93.99 

$`17Q 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-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-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       67.46        46.32        30.21        57.73        53.16        38.99 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV 
        0.46         2.43        40.93        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         0.82        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       182.93       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
        9.67        73.41        17.19        60.69        94.95         9.34 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       13.61         2.73        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99       118.65        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
        0.76        12.36         1.74         0.82         0.62         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       14.50         1.35         1.35         1.81        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        0.26        14.89         1.48        13.91         0.69        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.58        13.48        12.59        45.96         6.64         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.59         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN TCGA-EX-A1H5 
       23.70         0.10         0.07         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        7.92        14.70         4.47         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         3.52         1.32         1.97         1.12        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         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       36.36        14.43        16.64        19.33        20.48        15.58 
TCGA-JW-A852 TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A5YI TCGA-MU-A8JM 
        5.13         0.89         0.07         0.82         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A6DT 
       29.72         0.07         4.34         2.96         3.72         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD 
       11.67 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.10               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            100.14             182.93 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             13.46              13.58 
[1] "0.1 - 100.1 (13.5)" "0.0 - 182.9 (13.6)"
[1] "hr=" "1.4"
D31V2, continuous
                    vv
clus                 T1 T2+T3+T4
  17Q GAIN MUTATED    9        8
  17Q GAIN WILD-TYPE 88       31
D31V3, multiclass
          clus
vv         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                      9                 88
  T2+T3+T4                8                 31
[1] 2 2
[1] FALSE
D31V4, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    7  8
  17Q GAIN WILD-TYPE 80 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7    8
  17Q GAIN WILD-TYPE   80   32
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                7                 80
  1                8                 32
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED   12  0  7
  17Q GAIN WILD-TYPE 60  3 58
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               12                 60
  M1                0                  3
  MX                7                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED               0                               21
  17Q GAIN WILD-TYPE             2                              123
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17Q GAIN MUTATED                                               0
  17Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17Q GAIN MUTATED                                     5
  17Q GAIN WILD-TYPE                                  15
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17Q GAIN MUTATED                                           0
  17Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17Q GAIN MUTATED                                              0
  17Q GAIN WILD-TYPE                                            4
D31V6, multiclass
                                               clus
vv                                              17Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            21
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              17Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4  22
  17Q GAIN WILD-TYPE  23 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   22
  17Q GAIN WILD-TYPE   23  127
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 4                 23
  YES               22                127
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     3
  17Q GAIN WILD-TYPE                                7    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED                           1
  17Q GAIN WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    20
  17Q GAIN WILD-TYPE                                         1   110
D31V10, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    3                 12
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   20                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"
D31V11, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     2  17
  17Q GAIN WILD-TYPE   9 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2   17
  17Q GAIN WILD-TYPE    9  110
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               17                110
[1] 2 2
[1] FALSE
D31V12, continuous
D31V13, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    5  5
  17Q GAIN WILD-TYPE 43 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    5
  17Q GAIN WILD-TYPE   43   14
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  TUMOR FREE                5                 43
  WITH TUMOR                5                 14
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  17Q GAIN MUTATED         0      1       0            22       3
  17Q GAIN WILD-TYPE       1      9       6           125       9
D31V14, multiclass
               clus
vv              17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES               22                125
  VIETNAM                      3                  9
[1] 5 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                 G1 G2 G3 G4 GX
  17Q GAIN MUTATED    0 10 15  0  1
  17Q GAIN WILD-TYPE 14 73 57  1  4
D31V15, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  G1                0                 14
  G2               10                 73
  G3               15                 57
  G4                0                  1
  GX                1                  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"
D31V16, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 23 
        TCGA-BI-A0VR         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1ME         TCGA-C5-A1MF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A2M2         TCGA-C5-A3HD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-C5-A7CM         TCGA-C5-A7CO         TCGA-FU-A2QG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-HM-A3JK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LB 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-MU-A5YI         TCGA-MU-A8JM 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
D31V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17Q GAIN MUTATED                                             1
  17Q GAIN WILD-TYPE                                          20
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  17Q GAIN MUTATED                                        1
  17Q GAIN WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  17Q GAIN MUTATED                                                 0
  17Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17Q GAIN MUTATED                4                  16
  17Q GAIN WILD-TYPE             32                  67
D31V18, multiclass
                                                 clus
vv                                                17Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                           16
                                                 clus
vv                                                17Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  32
  LIFELONG NON-SMOKER                                             67
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  17Q GAIN MUTATED             2        6             2        0
  17Q GAIN WILD-TYPE          15       31             9        5
D31V20, multiclass
               clus
vv              17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COMBINATION                  2                 15
  EXTERNAL                     6                 31
  EXTERNAL BEAM                2                  9
  INTERNAL                     0                  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"
D31V21, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    1  0
  17Q GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    0
  17Q GAIN WILD-TYPE   10    3
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D31V22, continuous
D31V23, continuous
D31V24, continuous
D31V25, continuous
D31V26, continuous
D31V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  17Q GAIN MUTATED                                     0
  17Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  17Q GAIN MUTATED                                     1
  17Q GAIN WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  17Q GAIN MUTATED                         1                       0
  17Q GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17Q GAIN MUTATED                         0
  17Q GAIN WILD-TYPE                       5
D31V28, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 21 
        TCGA-C5-A0TN         TCGA-C5-A1BE         TCGA-C5-A1BM 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-DR-A0ZM         TCGA-DS-A0VK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EK-A2RN         TCGA-EK-A2RO 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A8JM         TCGA-UC-A7PD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
                    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                                                2
  17Q GAIN WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17Q GAIN MUTATED                                                                                   9
  17Q GAIN WILD-TYPE                                                                                45
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17Q GAIN MUTATED                                                                                             10
  17Q GAIN WILD-TYPE                                                                                           67
D31V29, multiclass
                                                                                              clus
vv                                                                                             17Q 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)               10
                                                                                              clus
vv                                                                                             17Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                8
  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)                 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"
D31V30, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    4 11
  17Q GAIN WILD-TYPE 50 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   11
  17Q GAIN WILD-TYPE   50   48
         clus
vv        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ABSENT                 4                 50
  PRESENT               11                 48
[1] 2 2
[1] FALSE
D31V31, continuous
D31V32, continuous
D31V33, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3 11
  17Q GAIN WILD-TYPE 32 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3   11
  17Q GAIN WILD-TYPE   32   70
                                          clus
vv                                         17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               11                 70
[1] 2 2
[1] FALSE
D31V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  17Q GAIN MUTATED       0                   14                   1
  17Q GAIN WILD-TYPE     3                   99                   4
D31V35, multiclass
                      clus
vv                     17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               14                 99
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17Q GAIN MUTATED              2           7          3
  17Q GAIN WILD-TYPE            6          33         37
D31V36, multiclass
              clus
vv             17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CURRENT USER                2                  6
  FORMER USER                 7                 33
  NEVER USED                  3                 37
[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, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    8  3
  17Q GAIN WILD-TYPE 65 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      8    3
  17Q GAIN WILD-TYPE   65   11
         clus
vv        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ABSENT                 8                 65
  PRESENT                3                 11
[1] 2 2
[1] FALSE
D31V39, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                  7 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM 
"17Q GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  17Q GAIN MUTATED     0    0   0    6    3  1   1    4    0   0   2  0  2
  17Q GAIN WILD-TYPE   2    1  22   45   18  2   5    2    8  13   0  1  5
D31V40, multiclass
      clus
vv     17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 0                 22
  T1B1                6                 45
  T1B2                3                 18
  T2                  1                  2
  T2A                 1                  5
  T2A1                4                  2
  T2A2                0                  8
  T2B                 0                 13
  T3B                 2                  0
  T4                  0                  1
  TX                  2                  5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V41, continuous

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    19   3
  18P GAIN WILD-TYPE 118  29
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                22                147 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 29 
$`18P GAIN MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A2LT 
       23.67       173.29        46.32        35.01        38.99        73.18 
TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-DR-A0ZL TCGA-DS-A3LQ 
      182.93         9.67        17.19        60.69        87.75        22.98 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2RO TCGA-FU-A3TX 
        1.35        14.50        13.91        14.96         0.07         1.48 
TCGA-HM-A3JK TCGA-JW-A5VK TCGA-MY-A5BF TCGA-Q1-A5R3 
       20.78        20.48         4.34         5.85 

$`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-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ 
       31.40        30.21        57.73        53.16        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX 
        2.43        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         0.82        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        25.35       101.82       134.33        15.48 
TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       73.41        85.55        94.95         9.34        13.61         2.73 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99       118.65        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18         7.33         8.28         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
        1.35         1.81        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
        1.48         0.69        14.99        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       45.96         6.64         0.53         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        0.03         0.36         1.18        23.70         2.24         0.10 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         4.47         6.12         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
        2.17         0.66         1.02         1.45         1.58         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         1.12        25.41 
TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       21.67        14.93         4.11       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       14.43        16.64        19.33        15.58        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        0.10         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42        29.72         0.07         2.96         3.72         3.45 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.07               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            182.93             177.04 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             20.63              12.59 
[1] "0.1 - 182.9 (20.6)" "0.0 - 177.0 (12.6)"
[1] "hr=" "2"  
D32V2, continuous
                    vv
clus                 T1 T2+T3+T4
  18P GAIN MUTATED   12        5
  18P GAIN WILD-TYPE 85       34
D32V3, multiclass
          clus
vv         18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                     12                 85
  T2+T3+T4                5                 34
[1] 2 2
[1] FALSE
D32V4, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   11  4
  18P GAIN WILD-TYPE 76 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     11    4
  18P GAIN WILD-TYPE   76   36
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               11                 76
  1                4                 36
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18P GAIN MUTATED   12  0  6
  18P GAIN WILD-TYPE 60  3 59
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               12                 60
  M1                0                  3
  MX                6                 59
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED               0                               21
  18P GAIN WILD-TYPE             2                              123
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18P GAIN MUTATED                                               1
  18P GAIN WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18P GAIN MUTATED                                     1
  18P GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18P GAIN MUTATED                                           0
  18P GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18P GAIN MUTATED                                              0
  18P GAIN WILD-TYPE                                            4
D32V6, multiclass
                                               clus
vv                                              18P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            21
  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                                              18P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     6  17
  18P GAIN WILD-TYPE  21 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6   17
  18P GAIN WILD-TYPE   21  132
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 6                 21
  YES               17                132
[1] 2 2
[1] FALSE
D32V8, continuous
D32V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  1     3
  18P GAIN WILD-TYPE                                6    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED                           1
  18P GAIN WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           0    16
  18P GAIN WILD-TYPE                                         1   114
D32V10, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  6
  ASIAN                                                    3                 12
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                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"
D32V11, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  17
  18P GAIN WILD-TYPE   9 110
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   17
  18P GAIN WILD-TYPE    9  110
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               17                110
[1] 2 2
[1] FALSE
D32V12, continuous
D32V13, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    8  3
  18P GAIN WILD-TYPE 40 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    3
  18P GAIN WILD-TYPE   40   16
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  TUMOR FREE                8                 40
  WITH TUMOR                3                 16
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  18P GAIN MUTATED         0      1       1            19       2
  18P GAIN WILD-TYPE       1      9       5           128      10
D32V14, multiclass
               clus
vv              18P GAIN MUTATED 18P GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      1                  5
  UNITED STATES               19                128
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  18P GAIN MUTATED    2  8 13  0  0
  18P GAIN WILD-TYPE 12 75 59  1  5
D32V15, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  G1                2                 12
  G2                8                 75
  G3               13                 59
  G4                0                  1
  GX                0                  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"
D32V16, continuous
D32V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18P GAIN MUTATED                                             4
  18P GAIN WILD-TYPE                                          17
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  18P GAIN MUTATED                                        3
  18P GAIN WILD-TYPE                                      5
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  18P GAIN MUTATED                                                 0
  18P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18P GAIN MUTATED                2                  10
  18P GAIN WILD-TYPE             34                  73
D32V18, multiclass
                                                 clus
vv                                                18P 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                                                 2
  LIFELONG NON-SMOKER                                           10
                                                 clus
vv                                                18P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  34
  LIFELONG NON-SMOKER                                             73
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  18P GAIN MUTATED             2        3             4        1
  18P GAIN WILD-TYPE          15       34             7        4
D32V20, multiclass
               clus
vv              18P GAIN MUTATED 18P GAIN WILD-TYPE
  COMBINATION                  2                 15
  EXTERNAL                     3                 34
  EXTERNAL BEAM                4                  7
  INTERNAL                     1                  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"
D32V21, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1  0
  18P GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    0
  18P GAIN WILD-TYPE   10    3
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D32V22, continuous
D32V23, continuous
D32V24, continuous
D32V25, continuous
D32V26, continuous
D32V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  18P GAIN MUTATED                                     1
  18P GAIN WILD-TYPE                                   1
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  18P GAIN MUTATED                                     1
  18P GAIN WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  18P GAIN MUTATED                         1                       0
  18P GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18P GAIN MUTATED                         0
  18P GAIN WILD-TYPE                       5
D32V28, multiclass
                                     clus
vv                                    18P GAIN MUTATED 18P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                1                  1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            1                  8
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  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)
  18P GAIN MUTATED                                               0
  18P GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18P GAIN MUTATED                                                1
  18P GAIN WILD-TYPE                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18P GAIN MUTATED                                                                                   9
  18P GAIN WILD-TYPE                                                                                45
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18P GAIN MUTATED                                                                                              8
  18P GAIN WILD-TYPE                                                                                           69
D32V29, multiclass
                                                                                              clus
vv                                                                                             18P 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)                8
                                                                                              clus
vv                                                                                             18P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                9
  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"
D32V30, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    8  6
  18P GAIN WILD-TYPE 46 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    6
  18P GAIN WILD-TYPE   46   53
         clus
vv        18P GAIN MUTATED 18P GAIN WILD-TYPE
  ABSENT                 8                 46
  PRESENT                6                 53
[1] 2 2
[1] FALSE
D32V31, continuous
D32V32, continuous
D32V33, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    6 12
  18P GAIN WILD-TYPE 29 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6   12
  18P GAIN WILD-TYPE   29   69
                                          clus
vv                                         18P GAIN MUTATED 18P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               12                 69
[1] 2 2
[1] FALSE
D32V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  18P GAIN MUTATED       1                   14                   0
  18P GAIN WILD-TYPE     2                   99                   5
D32V35, multiclass
                      clus
vv                     18P GAIN MUTATED 18P GAIN WILD-TYPE
  OTHER                               1                  2
  RADICAL HYSTERECTOMY               14                 99
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18P GAIN MUTATED              1           6          7
  18P GAIN WILD-TYPE            7          34         33
D32V36, multiclass
              clus
vv             18P GAIN MUTATED 18P GAIN WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 6                 34
  NEVER USED                  7                 33
[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, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    8  2
  18P GAIN WILD-TYPE 65 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    2
  18P GAIN WILD-TYPE   65   12
         clus
vv        18P GAIN MUTATED 18P GAIN WILD-TYPE
  ABSENT                 8                 65
  PRESENT                2                 12
[1] 2 2
[1] FALSE
D32V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  18P GAIN MUTATED     0    0   5    4    3  0   0    1    1   1   2  0  1
  18P GAIN WILD-TYPE   2    1  17   47   18  3   6    5    7  12   0  1  6
D32V40, multiclass
      clus
vv     18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 5                 17
  T1B1                4                 47
  T1B2                3                 18
  T2                  0                  3
  T2A                 0                  6
  T2A1                1                  5
  T2A2                1                  7
  T2B                 1                 12
  T3B                 2                  0
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V41, continuous

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    11   1
  18Q GAIN WILD-TYPE 126  31
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                157 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 31 
$`18Q GAIN MUTATED`
TCGA-C5-A1MH TCGA-C5-A2LT TCGA-C5-A7CG TCGA-C5-A7UH TCGA-DS-A3LQ TCGA-EA-A411 
       38.99        73.18       182.93        60.69        22.98         1.35 
TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EK-A2RO TCGA-FU-A3TX TCGA-HM-A3JK TCGA-JW-A5VK 
       14.50        14.96         0.07         1.48        20.78        20.48 

$`18Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-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-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         0.82        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-A7CO 
       25.35       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       17.19        85.55        94.95         9.34        13.61         2.73 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18         7.33         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       14.50         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       14.89         1.48        13.91         0.69        14.99        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.24         0.10         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70         4.47         6.12         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.12        25.41        21.67        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       26.56        36.36        14.43        16.64        19.33        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       10.06         5.13         0.10         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        2.96         3.72         3.45         5.85         3.39         3.72 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        5.75         4.80         6.25        19.59         3.88        11.67 
TCGA-UC-A7PF 
       93.99 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.07               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            182.93             177.04 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             20.63              12.82 
[1] "0.1 - 182.9 (20.6)" "0.0 - 177.0 (12.8)"
[1] "hr=" "3.1"
D33V2, continuous
                    vv
clus                 T1 T2+T3+T4
  18Q GAIN MUTATED    6        3
  18Q GAIN WILD-TYPE 91       36
D33V3, multiclass
          clus
vv         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                      6                 91
  T2+T3+T4                3                 36
[1] 2 2
[1] FALSE
D33V4, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  2
  18Q GAIN WILD-TYPE 82 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    2
  18Q GAIN WILD-TYPE   82   38
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                5                 82
  1                2                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18Q GAIN MUTATED    6  0  3
  18Q GAIN WILD-TYPE 66  3 62
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                6                 66
  M1                0                  3
  MX                3                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED               0                               12
  18Q GAIN WILD-TYPE             2                              132
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18Q GAIN MUTATED                                               0
  18Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18Q GAIN MUTATED                                     0
  18Q GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18Q GAIN MUTATED                                           0
  18Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18Q GAIN MUTATED                                              0
  18Q GAIN WILD-TYPE                                            4
D33V6, multiclass
                                               clus
vv                                              18Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  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                 0
                                               clus
vv                                              18Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             132
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4   8
  18Q GAIN WILD-TYPE  23 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    8
  18Q GAIN WILD-TYPE   23  141
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 4                 23
  YES                8                141
[1] 2 2
[1] FALSE
D33V8, continuous
D33V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  1     2
  18Q GAIN WILD-TYPE                                6    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED                           1
  18Q GAIN WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           0     6
  18Q GAIN WILD-TYPE                                         1   124
D33V10, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  6
  ASIAN                                                    2                 13
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    6                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"
D33V11, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1   9
  18Q GAIN WILD-TYPE  10 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    9
  18Q GAIN WILD-TYPE   10  118
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO                9                118
[1] 2 2
[1] FALSE
D33V12, continuous
D33V13, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  2
  18Q GAIN WILD-TYPE 45 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    2
  18Q GAIN WILD-TYPE   45   17
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  TUMOR FREE                3                 45
  WITH TUMOR                2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  18Q GAIN MUTATED         0      1       0             9       2
  18Q GAIN WILD-TYPE       1      9       6           138      10
D33V14, multiclass
               clus
vv              18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES                9                138
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  18Q GAIN MUTATED    1  3  8  0  0
  18Q GAIN WILD-TYPE 13 80 64  1  5
D33V15, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  G1                1                 13
  G2                3                 80
  G3                8                 64
  G4                0                  1
  GX                0                  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"
D33V16, continuous
D33V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18Q GAIN MUTATED                                             2
  18Q GAIN WILD-TYPE                                          19
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  18Q GAIN MUTATED                                        3
  18Q GAIN WILD-TYPE                                      5
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  18Q GAIN MUTATED                                                 0
  18Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18Q GAIN MUTATED                1                   5
  18Q GAIN WILD-TYPE             35                  78
D33V18, multiclass
                                                 clus
vv                                                18Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 1
  LIFELONG NON-SMOKER                                            5
                                                 clus
vv                                                18Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  35
  LIFELONG NON-SMOKER                                             78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  18Q GAIN MUTATED             1        0             3        1
  18Q GAIN WILD-TYPE          16       37             8        4
D33V20, multiclass
               clus
vv              18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COMBINATION                  1                 16
  EXTERNAL                     0                 37
  EXTERNAL BEAM                3                  8
  INTERNAL                     1                  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"
D33V21, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    0  0
  18Q GAIN WILD-TYPE 11  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    0
  18Q GAIN WILD-TYPE   11    3
D33V22, continuous
D33V23, continuous
D33V24, continuous
D33V25, continuous
D33V26, continuous
D33V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  18Q GAIN MUTATED                                     1
  18Q GAIN WILD-TYPE                                   1
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  18Q GAIN MUTATED                                     0
  18Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  18Q GAIN MUTATED                         1                       0
  18Q GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18Q GAIN MUTATED                         0
  18Q GAIN WILD-TYPE                       5
D33V28, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 21 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A2LX         TCGA-DR-A0ZM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-EA-A50E         TCGA-EK-A2RN 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A8JM         TCGA-UC-A7PD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    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                                                1
  18Q GAIN WILD-TYPE                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18Q GAIN MUTATED                                                                                   5
  18Q GAIN WILD-TYPE                                                                                49
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18Q GAIN MUTATED                                                                                              4
  18Q GAIN WILD-TYPE                                                                                           73
D33V29, multiclass
                                                                                              clus
vv                                                                                             18Q 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)                           5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                4
                                                                                              clus
vv                                                                                             18Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 73
[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"
D33V30, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  2
  18Q GAIN WILD-TYPE 49 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    2
  18Q GAIN WILD-TYPE   49   57
         clus
vv        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ABSENT                 5                 49
  PRESENT                2                 57
[1] 2 2
[1] FALSE
D33V31, continuous
D33V32, continuous
D33V33, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  5
  18Q GAIN WILD-TYPE 30 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    5
  18Q GAIN WILD-TYPE   30   76
                                          clus
vv                                         18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    5                 30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                5                 76
[1] 2 2
[1] FALSE
D33V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  18Q GAIN MUTATED       0                    8                   0
  18Q GAIN WILD-TYPE     3                  105                   5
D33V35, multiclass
                      clus
vv                     18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY                8                105
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18Q GAIN MUTATED              1           4          3
  18Q GAIN WILD-TYPE            7          36         37
D33V36, multiclass
              clus
vv             18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 4                 36
  NEVER USED                  3                 37
[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, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  1
  18Q GAIN WILD-TYPE 70 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    1
  18Q GAIN WILD-TYPE   70   13
         clus
vv        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ABSENT                 3                 70
  PRESENT                1                 13
[1] 2 2
[1] FALSE
D33V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  18Q GAIN MUTATED     0    0   2    2    2  0   0    1    0   1   1  0  0
  18Q GAIN WILD-TYPE   2    1  20   49   19  3   6    5    8  12   1  1  7
D33V40, multiclass
      clus
vv     18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 2                 20
  T1B1                2                 49
  T1B2                2                 19
  T2                  0                  3
  T2A                 0                  6
  T2A1                1                  5
  T2A2                0                  8
  T2B                 1                 12
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V41, continuous

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    20   5
  19P GAIN WILD-TYPE 117  27
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                25                144 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 27 
$`19P GAIN MUTATED`
TCGA-C5-A0TN TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A2LY TCGA-C5-A3HD 
       11.44        53.16        38.99        35.61        78.35        52.01 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7X5 TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WI 
      182.93        25.35        13.61         2.66        22.98         8.28 
TCGA-EA-A43B TCGA-EA-A5O9 TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RM TCGA-EK-A2RN 
        1.81        13.91        14.96         0.59         2.24         0.10 
TCGA-FU-A40J TCGA-HM-A3JK TCGA-IR-A3LL TCGA-JW-A852 TCGA-LP-A4AU TCGA-MY-A5BE 
        1.35        20.78        36.36         5.13         0.10         0.07 
TCGA-Q1-A5R3 
        5.85 

$`19P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        23.67        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-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
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-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE 
       73.45        83.05       100.14        38.43         0.82        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         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       73.41        17.19        85.55        60.69        94.95         9.34 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
        2.73        87.75        58.88        36.76       117.99       118.65 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.83        16.18         7.33         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35        14.50        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
       14.89         1.48         0.69        14.99        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RC 
       12.59        45.96         6.64         0.53         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.03         0.36         1.18        23.70         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        4.47         6.12         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.66         1.02         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        3.52         1.32         1.97         1.12        25.41        21.67 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI 
       96.95        78.71        81.96        26.56        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-LP-A4AW TCGA-LP-A4AX 
       19.33        20.48        15.58        10.06         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF 
        0.82        13.87         0.03         5.42        29.72         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96         3.72         3.45         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.07               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            182.93             177.04 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             13.61              13.53 
[1] "0.1 - 182.9 (13.6)" "0.0 - 177.0 (13.5)"
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 T1 T2+T3+T4
  19P GAIN MUTATED   12        7
  19P GAIN WILD-TYPE 85       32
D34V3, multiclass
          clus
vv         19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                     12                 85
  T2+T3+T4                7                 32
[1] 2 2
[1] FALSE
D34V4, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    8 10
  19P GAIN WILD-TYPE 79 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      8   10
  19P GAIN WILD-TYPE   79   30
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                8                 79
  1               10                 30
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19P GAIN MUTATED   10  0 10
  19P GAIN WILD-TYPE 62  3 55
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               10                 62
  M1                0                  3
  MX               10                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED               0                               25
  19P GAIN WILD-TYPE             2                              119
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19P GAIN MUTATED                                               0
  19P GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19P GAIN MUTATED                                     1
  19P GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19P GAIN MUTATED                                           0
  19P GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19P GAIN MUTATED                                              0
  19P GAIN WILD-TYPE                                            4
D34V6, multiclass
                                               clus
vv                                              19P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            25
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              19P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             119
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     7  19
  19P GAIN WILD-TYPE  20 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7   19
  19P GAIN WILD-TYPE   20  130
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 7                 20
  YES               19                130
[1] 2 2
[1] FALSE
D34V8, continuous
D34V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     2
  19P GAIN WILD-TYPE                                7    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED                           3
  19P GAIN WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           0    20
  19P GAIN WILD-TYPE                                         1   110
D34V10, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    2                 13
  BLACK OR AFRICAN AMERICAN                                3                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   20                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"
D34V11, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  20
  19P GAIN WILD-TYPE  10 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   20
  19P GAIN WILD-TYPE   10  107
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               20                107
[1] 2 2
[1] FALSE
D34V12, continuous
D34V13, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    6  5
  19P GAIN WILD-TYPE 42 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6    5
  19P GAIN WILD-TYPE   42   14
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  TUMOR FREE                6                 42
  WITH TUMOR                5                 14
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  19P GAIN MUTATED         0      0       2            22       2
  19P GAIN WILD-TYPE       1     10       4           125      10
D34V14, multiclass
               clus
vv              19P GAIN MUTATED 19P GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      2                  4
  UNITED STATES               22                125
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  19P GAIN MUTATED    0 15 11  0  0
  19P GAIN WILD-TYPE 14 68 61  1  5
D34V15, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  G1                0                 14
  G2               15                 68
  G3               11                 61
  G4                0                  1
  GX                0                  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"
D34V16, continuous
D34V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19P GAIN MUTATED                                             3
  19P GAIN WILD-TYPE                                          18
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  19P GAIN MUTATED                                        2
  19P GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  19P GAIN MUTATED                                                 0
  19P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19P GAIN MUTATED                1                  15
  19P GAIN WILD-TYPE             35                  68
D34V18, multiclass
                                                 clus
vv                                                19P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 1
  LIFELONG NON-SMOKER                                           15
                                                 clus
vv                                                19P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  35
  LIFELONG NON-SMOKER                                             68
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  19P GAIN MUTATED             4        5             3        0
  19P GAIN WILD-TYPE          13       32             8        5
D34V20, multiclass
               clus
vv              19P GAIN MUTATED 19P GAIN WILD-TYPE
  COMBINATION                  4                 13
  EXTERNAL                     5                 32
  EXTERNAL BEAM                3                  8
  INTERNAL                     0                  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"
D34V21, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    1  0
  19P GAIN WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    0
  19P GAIN WILD-TYPE   10    3
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D34V22, continuous
D34V23, continuous
D34V24, continuous
D34V25, continuous
D34V26, continuous
D34V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  19P GAIN MUTATED                                     0
  19P GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  19P GAIN MUTATED                                     1
  19P GAIN WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  19P GAIN MUTATED                         3                       0
  19P GAIN WILD-TYPE                       6                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19P GAIN MUTATED                         0
  19P GAIN WILD-TYPE                       5
D34V28, multiclass
                                     clus
vv                                    19P GAIN MUTATED 19P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            3                  6
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  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)
  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                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19P GAIN MUTATED                                                                                   7
  19P GAIN WILD-TYPE                                                                                47
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19P GAIN MUTATED                                                                                             12
  19P GAIN WILD-TYPE                                                                                           65
D34V29, 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)                           7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               12
                                                                                              clus
vv                                                                                             19P GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                8
  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)                 65
[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"
D34V30, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    6 10
  19P GAIN WILD-TYPE 48 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6   10
  19P GAIN WILD-TYPE   48   49
         clus
vv        19P GAIN MUTATED 19P GAIN WILD-TYPE
  ABSENT                 6                 48
  PRESENT               10                 49
[1] 2 2
[1] FALSE
D34V31, continuous
D34V32, continuous
D34V33, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    9  8
  19P GAIN WILD-TYPE 26 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      9    8
  19P GAIN WILD-TYPE   26   73
                                          clus
vv                                         19P GAIN MUTATED 19P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                8                 73
[1] 2 2
[1] FALSE
D34V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  19P GAIN MUTATED       0                   16                   1
  19P GAIN WILD-TYPE     3                   97                   4
D34V35, multiclass
                      clus
vv                     19P GAIN MUTATED 19P GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               16                 97
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19P GAIN MUTATED              1           6          6
  19P GAIN WILD-TYPE            7          34         34
D34V36, multiclass
              clus
vv             19P GAIN MUTATED 19P GAIN WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 6                 34
  NEVER USED                  6                 34
[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, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    9  0
  19P GAIN WILD-TYPE 64 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      9    0
  19P GAIN WILD-TYPE   64   14
         clus
vv        19P GAIN MUTATED 19P GAIN WILD-TYPE
  ABSENT                 9                 64
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D34V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  19P GAIN MUTATED     0    0   2    8    2  1   0    1    1   3   1  0  1
  19P GAIN WILD-TYPE   2    1  20   43   19  2   6    5    7  10   1  1  6
D34V40, multiclass
      clus
vv     19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 2                 20
  T1B1                8                 43
  T1B2                2                 19
  T2                  1                  2
  T2A                 0                  6
  T2A1                1                  5
  T2A2                1                  7
  T2B                 3                 10
  T3B                 1                  1
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V41, continuous

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    28   9
  19Q GAIN WILD-TYPE 109  23
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                37                132 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                 23 
$`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       182.93 
TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CO TCGA-C5-A7X3 TCGA-DS-A0VL TCGA-DS-A3LQ 
       25.35       134.33        73.41         9.34         2.66        22.98 
TCGA-DS-A7WI TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A5O9 
        8.28        14.50         1.35        14.50         1.81        13.91 
TCGA-EA-A5ZF TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-FU-A40J 
       14.96         0.59         1.18         2.24         0.10         1.35 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LL TCGA-JW-A852 TCGA-MY-A5BE TCGA-PN-A8MA 
       21.67        20.78        36.36         5.13         0.07         2.96 
TCGA-Q1-A5R3 
        5.85 

$`19Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        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-A1M6 
      177.04       173.29        82.85        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A1MP 
       46.32        30.21        35.01         0.46        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        73.45        83.05       100.14        38.43         0.82 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM 
       18.02        17.85        20.42       101.82        15.48         9.67 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 
       17.19        85.55        60.69        94.95        13.61         2.73 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ 
       87.75        58.88        36.76       117.99       118.65        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18         7.33         0.76        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A44S 
        0.82         0.62        13.05         1.18         1.35        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26        14.89         1.48         0.69        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG 
       13.58        13.48        12.59        45.96         6.64         0.53 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO 
        0.07         4.04         0.03         0.36        23.70         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         4.47         6.12         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         3.52         1.32         1.97         1.12        25.41 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI 
       96.95        78.71        81.96        26.56        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AW 
       19.33        20.48        15.58        10.06         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34         3.72         3.45         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.07               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            182.93             177.04 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            14.500             13.265 
[1] "0.1 - 182.9 (14.5)" "0.0 - 177.0 (13.3)"
[1] "hr=" "1.4"
D35V2, continuous
                    vv
clus                 T1 T2+T3+T4
  19Q GAIN MUTATED   19        8
  19Q GAIN WILD-TYPE 78       31
D35V3, multiclass
          clus
vv         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                     19                 78
  T2+T3+T4                8                 31
[1] 2 2
[1] FALSE
D35V4, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   16 10
  19Q GAIN WILD-TYPE 71 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     16   10
  19Q GAIN WILD-TYPE   71   30
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               16                 71
  1               10                 30
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19Q GAIN MUTATED   16  0 12
  19Q GAIN WILD-TYPE 56  3 53
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               16                 56
  M1                0                  3
  MX               12                 53
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED               0                               38
  19Q GAIN WILD-TYPE             2                              106
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19Q GAIN MUTATED                                               0
  19Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19Q GAIN MUTATED                                     2
  19Q GAIN WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19Q GAIN MUTATED                                           0
  19Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19Q GAIN MUTATED                                              0
  19Q GAIN WILD-TYPE                                            4
D35V6, multiclass
                                               clus
vv                                              19Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            38
  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                                              19Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             106
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    11  29
  19Q GAIN WILD-TYPE  16 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     11   29
  19Q GAIN WILD-TYPE   16  120
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                11                 16
  YES               29                120
[1] 2 2
[1] FALSE
D35V8, continuous
D35V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     2
  19Q GAIN WILD-TYPE                                7    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED                           4
  19Q GAIN WILD-TYPE                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           0    33
  19Q GAIN WILD-TYPE                                         1    97
D35V10, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    2                 13
  BLACK OR AFRICAN AMERICAN                                4                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   33                 97
[1] 5 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 32
  19Q GAIN WILD-TYPE 10 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   32
  19Q GAIN WILD-TYPE   10   95
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               32                 95
[1] 2 2
[1] FALSE
D35V12, continuous
D35V13, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   11  8
  19Q GAIN WILD-TYPE 37 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     11    8
  19Q GAIN WILD-TYPE   37   11
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  TUMOR FREE               11                 37
  WITH TUMOR                8                 11
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  19Q GAIN MUTATED         1      1       3            33       2
  19Q GAIN WILD-TYPE       0      9       3           114      10
D35V14, multiclass
               clus
vv              19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      3                  3
  UNITED STATES               33                114
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  19Q GAIN MUTATED    1 19 19  0  0
  19Q GAIN WILD-TYPE 13 64 53  1  5
D35V15, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  G1                1                 13
  G2               19                 64
  G3               19                 53
  G4                0                  1
  GX                0                  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"
D35V16, continuous
D35V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19Q GAIN MUTATED                                             4
  19Q GAIN WILD-TYPE                                          17
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  19Q GAIN MUTATED                                        3
  19Q GAIN WILD-TYPE                                      5
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  19Q GAIN MUTATED                                                 1
  19Q GAIN WILD-TYPE                                               0
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19Q GAIN MUTATED                3                  19
  19Q GAIN WILD-TYPE             33                  64
D35V18, multiclass
                                                 clus
vv                                                19Q 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                                                 3
  LIFELONG NON-SMOKER                                           19
                                                 clus
vv                                                19Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  0
  CURRENT SMOKER                                                  33
  LIFELONG NON-SMOKER                                             64
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  19Q GAIN MUTATED             6        8             5        1
  19Q GAIN WILD-TYPE          11       29             6        4
D35V20, multiclass
               clus
vv              19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COMBINATION                  6                 11
  EXTERNAL                     8                 29
  EXTERNAL BEAM                5                  6
  INTERNAL                     1                  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"
D35V21, binary
                    cls
clus                 0 1
  19Q GAIN MUTATED   3 0
  19Q GAIN WILD-TYPE 8 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3    0
  19Q GAIN WILD-TYPE    8    3
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CGY                3                  8
  GY                 0                  3
[1] 2 2
[1] FALSE
D35V22, continuous
D35V23, continuous
D35V24, continuous
D35V25, continuous
D35V26, continuous
D35V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  19Q GAIN MUTATED                                     0
  19Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  19Q GAIN MUTATED                                     2
  19Q GAIN WILD-TYPE                                   4
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  19Q GAIN MUTATED                         3                       0
  19Q GAIN WILD-TYPE                       6                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19Q GAIN MUTATED                         0
  19Q GAIN WILD-TYPE                       5
D35V28, multiclass
                                     clus
vv                                    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  4
  OTHER LOCATION, SPECIFY                            3                  6
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  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)
  19Q GAIN MUTATED                                               0
  19Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  19Q GAIN MUTATED                                                2
  19Q GAIN WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19Q GAIN MUTATED                                                                                  10
  19Q GAIN WILD-TYPE                                                                                44
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19Q GAIN MUTATED                                                                                             18
  19Q GAIN WILD-TYPE                                                                                           59
D35V29, multiclass
                                                                                              clus
vv                                                                                             19Q 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)                          10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               18
                                                                                              clus
vv                                                                                             19Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                8
  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)                 59
[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"
D35V30, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   10 15
  19Q GAIN WILD-TYPE 44 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     10   15
  19Q GAIN WILD-TYPE   44   44
         clus
vv        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ABSENT                10                 44
  PRESENT               15                 44
[1] 2 2
[1] FALSE
D35V31, continuous
D35V32, continuous
D35V33, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   11 18
  19Q GAIN WILD-TYPE 24 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     11   18
  19Q GAIN WILD-TYPE   24   63
                                          clus
vv                                         19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   11                 24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               18                 63
[1] 2 2
[1] FALSE
D35V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  19Q GAIN MUTATED       0                   24                   1
  19Q GAIN WILD-TYPE     3                   89                   4
D35V35, multiclass
                      clus
vv                     19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               24                 89
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19Q GAIN MUTATED              2          10          8
  19Q GAIN WILD-TYPE            6          30         32
D35V36, multiclass
              clus
vv             19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CURRENT USER                2                  6
  FORMER USER                10                 30
  NEVER USED                  8                 32
[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, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   13  2
  19Q GAIN WILD-TYPE 60 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13    2
  19Q GAIN WILD-TYPE   60   12
         clus
vv        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ABSENT                13                 60
  PRESENT                2                 12
[1] 2 2
[1] FALSE
D35V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  19Q GAIN MUTATED     0    0   4   12    3  0   0    2    1   4   1  0  1
  19Q GAIN WILD-TYPE   2    1  18   39   18  3   6    4    7   9   1  1  6
D35V40, multiclass
      clus
vv     19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 4                 18
  T1B1               12                 39
  T1B2                3                 18
  T2                  0                  3
  T2A                 0                  6
  T2A1                2                  4
  T2A2                1                  7
  T2B                 4                  9
  T3B                 1                  1
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V41, continuous

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   48 10
  20P GAIN WILD-TYPE 89 22
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                58                111 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                 22 
$`20P GAIN MUTATED`
TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME 
      144.16       173.29        67.46        31.40        35.01        57.73 
TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LT TCGA-C5-A2LV 
       35.61         0.46        40.93         3.58        73.18        73.45 
TCGA-C5-A2LZ TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      100.14       182.93        25.35         9.67        73.41        17.19 
TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-DS-A0VK TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A1QS 
       60.69         2.73        36.76        22.98         7.33         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3QD TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5FO 
        1.74         0.82        13.05        14.50        14.89         1.48 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RJ 
       14.96        13.58        12.59         0.53         0.59         1.18 
TCGA-EK-A2RM TCGA-EK-A3GN TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI 
        2.24         0.03         1.22        23.84         2.17         1.45 
TCGA-FU-A40J TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-JW-A5VK 
        1.35        21.67        20.78       147.39        96.95        20.48 
TCGA-JW-A69B TCGA-LP-A4AX TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       10.06         0.07         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-RA-A741 TCGA-UC-A7PF 
        3.39         5.75         3.88        93.99 

$`20P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        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-A1M7 
       36.56       177.04        82.85         5.46        19.86        46.32 
TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A2LS TCGA-C5-A2LX 
       30.21        53.16        38.99         2.43        44.22        83.05 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35        38.43         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7UE TCGA-C5-A7UI 
       20.42       101.82       134.33        15.48        85.55        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
        9.34        13.61        87.75        58.88         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HR 
      118.65        16.83        16.18         8.28        12.36         1.32 
TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
        0.62         1.18        14.50         1.35         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.66        12.82         0.26        13.91         0.69        14.99 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       13.48        45.96         6.64         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.36        23.70         0.10         0.07         0.10         0.10 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.92         0.66         1.02         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A4S6 
        3.52         1.32         1.97         1.12        25.41        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH TCGA-IR-A3LI 
        4.11       137.16        66.81       117.40        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       26.56        36.36        14.43        16.64        19.33        15.58 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        5.13         0.10         0.89         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV TCGA-Q1-A73P 
        5.42        29.72         0.07         4.34         3.72         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD 
        6.25        19.59        11.67 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.03               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            182.93             177.04 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            13.315             13.610 
[1] "0.0 - 182.9 (13.3)" "0.0 - 177.0 (13.6)"
[1] "hr=" "1.3"
D36V2, continuous
                    vv
clus                 T1 T2+T3+T4
  20P GAIN MUTATED   31       10
  20P GAIN WILD-TYPE 66       29
D36V3, multiclass
          clus
vv         20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                     31                 66
  T2+T3+T4               10                 29
[1] 2 2
[1] FALSE
D36V4, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   21 17
  20P GAIN WILD-TYPE 66 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     21   17
  20P GAIN WILD-TYPE   66   23
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               21                 66
  1               17                 23
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED   25  0 20
  20P GAIN WILD-TYPE 47  3 45
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               25                 47
  M1                0                  3
  MX               20                 45
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED               0                               47
  20P GAIN WILD-TYPE             2                               97
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20P GAIN MUTATED                                               2
  20P GAIN WILD-TYPE                                             2
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20P GAIN MUTATED                                     8
  20P GAIN WILD-TYPE                                  12
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20P GAIN MUTATED                                           1
  20P GAIN WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20P GAIN MUTATED                                              2
  20P GAIN WILD-TYPE                                            2
D36V6, multiclass
                                               clus
vv                                              20P GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            47
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          8
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              20P GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                              97
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           12
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   2
[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"
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   10 50
  20P GAIN WILD-TYPE 17 99
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     10   50
  20P GAIN WILD-TYPE   17   99
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                10                 17
  YES               50                 99
[1] 2 2
[1] FALSE
D36V8, continuous
D36V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     4
  20P GAIN WILD-TYPE                                7    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED                           7
  20P GAIN WILD-TYPE                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           0    47
  20P GAIN WILD-TYPE                                         1    83
D36V10, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    4                 11
  BLACK OR AFRICAN AMERICAN                                7                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   47                 83
[1] 5 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    3 45
  20P GAIN WILD-TYPE  8 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   45
  20P GAIN WILD-TYPE    8   82
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               45                 82
[1] 2 2
[1] FALSE
D36V12, continuous
D36V13, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   15  7
  20P GAIN WILD-TYPE 33 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     15    7
  20P GAIN WILD-TYPE   33   12
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  TUMOR FREE               15                 33
  WITH TUMOR                7                 12
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  20P GAIN MUTATED         1      4       1            50       4
  20P GAIN WILD-TYPE       0      6       5            97       8
D36V14, multiclass
               clus
vv              20P GAIN MUTATED 20P GAIN WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       4                  6
  UKRAINE                      1                  5
  UNITED STATES               50                 97
  VIETNAM                      4                  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                 G1 G2 G3 G4 GX
  20P GAIN MUTATED    2 25 29  0  4
  20P GAIN WILD-TYPE 12 58 43  1  1
D36V15, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  G1                2                 12
  G2               25                 58
  G3               29                 43
  G4                0                  1
  GX                4                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V16, continuous
D36V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20P GAIN MUTATED                                             9
  20P GAIN WILD-TYPE                                          12
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  20P GAIN MUTATED                                        3
  20P GAIN WILD-TYPE                                      5
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  20P GAIN MUTATED                                                 0
  20P GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20P GAIN MUTATED               10                  28
  20P GAIN WILD-TYPE             26                  55
D36V18, multiclass
                                                 clus
vv                                                20P GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                10
  LIFELONG NON-SMOKER                                           28
                                                 clus
vv                                                20P GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  26
  LIFELONG NON-SMOKER                                             55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  20P GAIN MUTATED             6       11             6        3
  20P GAIN WILD-TYPE          11       26             5        2
D36V20, multiclass
               clus
vv              20P GAIN MUTATED 20P GAIN WILD-TYPE
  COMBINATION                  6                 11
  EXTERNAL                    11                 26
  EXTERNAL BEAM                6                  5
  INTERNAL                     3                  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"
D36V21, binary
                    cls
clus                 0 1
  20P GAIN MUTATED   5 1
  20P GAIN WILD-TYPE 6 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    1
  20P GAIN WILD-TYPE    6    2
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  CGY                5                  6
  GY                 1                  2
[1] 2 2
[1] FALSE
D36V22, continuous
D36V23, continuous
D36V24, continuous
D36V25, continuous
D36V26, continuous
D36V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  20P GAIN MUTATED                                     0
  20P GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  20P GAIN MUTATED                                     0
  20P GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  20P GAIN MUTATED                         1                       0
  20P GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20P GAIN MUTATED                         2
  20P GAIN WILD-TYPE                       3
D36V28, multiclass
                                     clus
vv                                    20P GAIN MUTATED 20P GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            1                  8
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  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)
  20P GAIN MUTATED                                               1
  20P GAIN WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  20P GAIN MUTATED                                                4
  20P GAIN WILD-TYPE                                              6
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20P GAIN MUTATED                                                                                  19
  20P GAIN WILD-TYPE                                                                                35
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20P GAIN MUTATED                                                                                             27
  20P GAIN WILD-TYPE                                                                                           50
D36V29, multiclass
                                                                                              clus
vv                                                                                             20P GAIN 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)                          19
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               27
                                                                                              clus
vv                                                                                             20P GAIN WILD-TYPE
  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)                            35
  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"
D36V30, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   16 21
  20P GAIN WILD-TYPE 38 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     16   21
  20P GAIN WILD-TYPE   38   38
         clus
vv        20P GAIN MUTATED 20P GAIN WILD-TYPE
  ABSENT                16                 38
  PRESENT               21                 38
[1] 2 2
[1] FALSE
D36V31, continuous
D36V32, continuous
D36V33, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   10 24
  20P GAIN WILD-TYPE 25 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     10   24
  20P GAIN WILD-TYPE   25   57
                                          clus
vv                                         20P GAIN MUTATED 20P GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   10                 25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               24                 57
[1] 2 2
[1] FALSE
D36V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  20P GAIN MUTATED       0                   36                   2
  20P GAIN WILD-TYPE     3                   77                   3
D36V35, multiclass
                      clus
vv                     20P GAIN MUTATED 20P GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               36                 77
  SIMPLE HYSTERECTOMY                 2                  3
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20P GAIN MUTATED              3          15         12
  20P GAIN WILD-TYPE            5          25         28
D36V36, multiclass
              clus
vv             20P GAIN MUTATED 20P GAIN WILD-TYPE
  CURRENT USER                3                  5
  FORMER USER                15                 25
  NEVER USED                 12                 28
[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, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   24  3
  20P GAIN WILD-TYPE 49 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     24    3
  20P GAIN WILD-TYPE   49   11
         clus
vv        20P GAIN MUTATED 20P GAIN WILD-TYPE
  ABSENT                24                 49
  PRESENT                3                 11
[1] 2 2
[1] FALSE
D36V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  20P GAIN MUTATED     0    0   7   20    4  0   2    3    0   3   2  0  5
  20P GAIN WILD-TYPE   2    1  15   31   17  3   4    3    8  10   0  1  2
D36V40, multiclass
      clus
vv     20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 7                 15
  T1B1               20                 31
  T1B2                4                 17
  T2                  0                  3
  T2A                 2                  4
  T2A1                3                  3
  T2A2                0                  8
  T2B                 3                 10
  T3B                 2                  0
  T4                  0                  1
  TX                  5                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V41, continuous

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   52  9
  20Q GAIN WILD-TYPE 85 23
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                61                108 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 9                 23 
$`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       182.93        25.35         9.67        17.19 
TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-DS-A3LQ TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A1QT 
       60.69         2.73        22.98         7.33         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5FO 
        1.74         1.32         0.82        14.50        14.89         1.48 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 
       14.96        13.58        12.59        45.96         0.53         0.59 
TCGA-EK-A2RJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO 
        1.18         0.10         0.03         1.22        23.84         2.17 
TCGA-FU-A3HY TCGA-FU-A3NI TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3L7 TCGA-IR-A3LF 
        0.66         1.45        21.67        20.78       147.39        96.95 
TCGA-IR-A3LH TCGA-JW-A5VK TCGA-JW-A69B TCGA-LP-A4AX TCGA-PN-A8MA TCGA-Q1-A5R1 
       78.71        20.48        10.06         0.07         2.96         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-RA-A741 
        3.45         5.85         3.39         5.75         4.80         3.88 
TCGA-UC-A7PF 
       93.99 

$`20Q GAIN WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK 
       23.67        11.44        68.84        18.74        36.56       177.04 
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-A2LS TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       53.16        38.99        44.22        73.45        83.05        78.35 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43         0.82        52.01        18.02        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI 
      101.82       134.33        15.48        73.41        85.55        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        9.34        13.61        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A3HT 
      117.99       118.65        16.83        16.18         8.28         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       13.05         1.18        14.50         1.35         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.66        12.82         0.26        13.91         0.69        14.99 
TCGA-EA-A78R TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
       13.48         6.64         0.07         4.04         0.03         0.36 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EX-A1H5 
       23.70         2.24         0.10         0.07         0.10        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A2QG 
        7.92         6.94        14.70         4.47         6.12         0.92 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.02         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.32         1.97         1.12        25.41        14.93         4.11 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      137.16        66.81       117.40        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU 
       14.43        16.64        19.33        15.58         5.13         0.10 
TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.89         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A6DV TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD 
        0.07         4.34         3.72         6.25        19.59        11.67 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.03               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            182.93             177.04 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             12.36              13.89 
[1] "0.0 - 182.9 (12.4)" "0.0 - 177.0 (13.9)"
[1] "hr=" "1.5"
D37V2, continuous
                    vv
clus                 T1 T2+T3+T4
  20Q GAIN MUTATED   33       12
  20Q GAIN WILD-TYPE 64       27
D37V3, multiclass
          clus
vv         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                     33                 64
  T2+T3+T4               12                 27
[1] 2 2
[1] FALSE
D37V4, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   27 15
  20Q GAIN WILD-TYPE 60 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     27   15
  20Q GAIN WILD-TYPE   60   25
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               27                 60
  1               15                 25
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   28  0 21
  20Q GAIN WILD-TYPE 44  3 44
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               28                 44
  M1                0                  3
  MX               21                 44
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED               0                               50
  20Q GAIN WILD-TYPE             2                               94
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20Q GAIN MUTATED                                               2
  20Q GAIN WILD-TYPE                                             2
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20Q GAIN MUTATED                                     9
  20Q GAIN WILD-TYPE                                  11
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20Q GAIN MUTATED                                           1
  20Q GAIN WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20Q GAIN MUTATED                                              2
  20Q GAIN WILD-TYPE                                            2
D37V6, multiclass
                                               clus
vv                                              20Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            50
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              20Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                              94
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  2
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   2
[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"
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   11 53
  20Q GAIN WILD-TYPE 16 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11   53
  20Q GAIN WILD-TYPE   16   96
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                11                 16
  YES               53                 96
[1] 2 2
[1] FALSE
D37V8, continuous
D37V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     5
  20Q GAIN WILD-TYPE                                7    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED                           7
  20Q GAIN WILD-TYPE                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           0    50
  20Q GAIN WILD-TYPE                                         1    80
D37V10, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    5                 10
  BLACK OR AFRICAN AMERICAN                                7                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   50                 80
[1] 5 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    3 47
  20Q GAIN WILD-TYPE  8 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3   47
  20Q GAIN WILD-TYPE    8   80
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               47                 80
[1] 2 2
[1] FALSE
D37V12, continuous
D37V13, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   16  7
  20Q GAIN WILD-TYPE 32 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     16    7
  20Q GAIN WILD-TYPE   32   12
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  TUMOR FREE               16                 32
  WITH TUMOR                7                 12
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  20Q GAIN MUTATED         1      6       1            51       5
  20Q GAIN WILD-TYPE       0      4       5            96       7
D37V14, multiclass
               clus
vv              20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       6                  4
  UKRAINE                      1                  5
  UNITED STATES               51                 96
  VIETNAM                      5                  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                 G1 G2 G3 G4 GX
  20Q GAIN MUTATED    3 27 29  1  4
  20Q GAIN WILD-TYPE 11 56 43  0  1
D37V15, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  G1                3                 11
  G2               27                 56
  G3               29                 43
  G4                1                  0
  GX                4                  1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V16, continuous
D37V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20Q GAIN MUTATED                                            10
  20Q GAIN WILD-TYPE                                          11
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  20Q GAIN MUTATED                                        2
  20Q GAIN WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  20Q GAIN MUTATED                                                 0
  20Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20Q GAIN MUTATED               11                  30
  20Q GAIN WILD-TYPE             25                  53
D37V18, multiclass
                                                 clus
vv                                                20Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   10
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                11
  LIFELONG NON-SMOKER                                           30
                                                 clus
vv                                                20Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     11
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  25
  LIFELONG NON-SMOKER                                             53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  20Q GAIN MUTATED             6       11             5        2
  20Q GAIN WILD-TYPE          11       26             6        3
D37V20, multiclass
               clus
vv              20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COMBINATION                  6                 11
  EXTERNAL                    11                 26
  EXTERNAL BEAM                5                  6
  INTERNAL                     2                  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"
D37V21, binary
                    cls
clus                 0 1
  20Q GAIN MUTATED   5 1
  20Q GAIN WILD-TYPE 6 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5    1
  20Q GAIN WILD-TYPE    6    2
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CGY                5                  6
  GY                 1                  2
[1] 2 2
[1] FALSE
D37V22, continuous
D37V23, continuous
D37V24, continuous
D37V25, continuous
D37V26, continuous
D37V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  20Q GAIN MUTATED                                     0
  20Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  20Q GAIN MUTATED                                     0
  20Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  20Q GAIN MUTATED                         1                       0
  20Q GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20Q GAIN MUTATED                         2
  20Q GAIN WILD-TYPE                       3
D37V28, multiclass
                                     clus
vv                                    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            1                  8
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  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)
  20Q GAIN MUTATED                                               0
  20Q GAIN WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  20Q GAIN MUTATED                                                4
  20Q GAIN WILD-TYPE                                              6
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20Q GAIN MUTATED                                                                                  21
  20Q GAIN WILD-TYPE                                                                                33
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20Q GAIN MUTATED                                                                                             29
  20Q GAIN WILD-TYPE                                                                                           48
D37V29, multiclass
                                                                                              clus
vv                                                                                             20Q 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)                          21
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               29
                                                                                              clus
vv                                                                                             20Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                6
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            33
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 48
[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"
D37V30, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   20 19
  20Q GAIN WILD-TYPE 34 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     20   19
  20Q GAIN WILD-TYPE   34   40
         clus
vv        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ABSENT                20                 34
  PRESENT               19                 40
[1] 2 2
[1] FALSE
D37V31, continuous
D37V32, continuous
D37V33, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    9 28
  20Q GAIN WILD-TYPE 26 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      9   28
  20Q GAIN WILD-TYPE   26   53
                                          clus
vv                                         20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               28                 53
[1] 2 2
[1] FALSE
D37V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  20Q GAIN MUTATED       0                   39                   2
  20Q GAIN WILD-TYPE     3                   74                   3
D37V35, multiclass
                      clus
vv                     20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               39                 74
  SIMPLE HYSTERECTOMY                 2                  3
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20Q GAIN MUTATED              4          17         12
  20Q GAIN WILD-TYPE            4          23         28
D37V36, multiclass
              clus
vv             20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CURRENT USER                4                  4
  FORMER USER                17                 23
  NEVER USED                 12                 28
[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, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   25  4
  20Q GAIN WILD-TYPE 48 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     25    4
  20Q GAIN WILD-TYPE   48   10
         clus
vv        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ABSENT                25                 48
  PRESENT                4                 10
[1] 2 2
[1] FALSE
D37V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  20Q GAIN MUTATED     0    0   8   20    5  0   3    3    0   4   2  0  5
  20Q GAIN WILD-TYPE   2    1  14   31   16  3   3    3    8   9   0  1  2
D37V40, multiclass
      clus
vv     20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 8                 14
  T1B1               20                 31
  T1B2                5                 16
  T2                  0                  3
  T2A                 3                  3
  T2A1                3                  3
  T2A2                0                  8
  T2B                 4                  9
  T3B                 2                  0
  T4                  0                  1
  TX                  5                  2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V41, continuous

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    12   7
  21Q GAIN WILD-TYPE 125  25
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                150 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 25 
$`21Q GAIN MUTATED`
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M6 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK 
        5.46        19.86        31.40        38.99        35.61         2.43 
TCGA-C5-A1MP TCGA-C5-A2LZ TCGA-C5-A7X8 TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A5O9 
        3.58       100.14         2.73         0.76         1.74        13.91 
TCGA-EK-A2RM TCGA-FU-A3TX TCGA-HM-A3JK TCGA-IR-A3LL TCGA-JW-A5VJ TCGA-LP-A4AU 
        2.24         1.48        20.78        36.36        19.33         0.10 
TCGA-MY-A5BE 
        0.07 

$`21Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-A1M5 
       36.56       144.16       177.04       173.29        82.85        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ 
       46.32        30.21        35.01        57.73        53.16         0.46 
TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LY 
       40.93        44.22        73.18        73.45        83.05        78.35 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43         0.82        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 
      182.93        25.35       101.82       134.33        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       73.41        17.19        85.55        60.69        94.95         9.34 
TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       13.61        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      118.65        22.98        16.83        16.18         7.33         8.28 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       12.36         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26        14.89         1.48         0.69        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.96        13.58        13.48        12.59        45.96         6.64 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.53         0.59         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        1.18        23.70         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.12         1.22        23.84         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.02         1.45         1.58         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 
        1.32         1.97         1.12        25.41        21.67        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK 
       78.71        81.96        26.56        14.43        16.64        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       15.58        10.06         5.13         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF TCGA-PN-A8MA 
       13.87         0.03         5.42        29.72         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        3.72         3.45         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.07               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            100.14             182.93 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             5.460             13.595 
[1] "0.1 - 100.1 (5.5)"  "0.0 - 182.9 (13.6)"
[1] "hr=" "3.3"
D38V2, continuous
                    vv
clus                 T1 T2+T3+T4
  21Q GAIN MUTATED    8        5
  21Q GAIN WILD-TYPE 89       34
D38V3, multiclass
          clus
vv         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                      8                 89
  T2+T3+T4                5                 34
[1] 2 2
[1] FALSE
D38V4, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    7  5
  21Q GAIN WILD-TYPE 80 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7    5
  21Q GAIN WILD-TYPE   80   35
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                7                 80
  1                5                 35
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  21Q GAIN MUTATED    8  0  5
  21Q GAIN WILD-TYPE 64  3 60
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                8                 64
  M1                0                  3
  MX                5                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED               0                               21
  21Q GAIN WILD-TYPE             2                              123
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  21Q GAIN MUTATED                                               0
  21Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  21Q GAIN MUTATED                                     0
  21Q GAIN WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  21Q GAIN MUTATED                                           0
  21Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  21Q GAIN MUTATED                                              1
  21Q GAIN WILD-TYPE                                            3
D38V6, multiclass
                                               clus
vv                                              21Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            21
  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                                              21Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     6  16
  21Q GAIN WILD-TYPE  21 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      6   16
  21Q GAIN WILD-TYPE   21  133
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 6                 21
  YES               16                133
[1] 2 2
[1] FALSE
D38V8, continuous
D38V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1     1
  21Q GAIN WILD-TYPE                                6    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED                           2
  21Q GAIN WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           0    17
  21Q GAIN WILD-TYPE                                         1   113
D38V10, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  6
  ASIAN                                                    1                 14
  BLACK OR AFRICAN AMERICAN                                2                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   17                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"
D38V11, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  16
  21Q GAIN WILD-TYPE  10 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   16
  21Q GAIN WILD-TYPE   10  111
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               16                111
[1] 2 2
[1] FALSE
D38V12, continuous
D38V13, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    5  7
  21Q GAIN WILD-TYPE 43 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5    7
  21Q GAIN WILD-TYPE   43   12
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  TUMOR FREE                5                 43
  WITH TUMOR                7                 12
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  21Q GAIN MUTATED         0      2       1            18       1
  21Q GAIN WILD-TYPE       1      8       5           129      11
D38V14, multiclass
               clus
vv              21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       2                  8
  UKRAINE                      1                  5
  UNITED STATES               18                129
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  21Q GAIN MUTATED    0  9 13  0  0
  21Q GAIN WILD-TYPE 14 74 59  1  5
D38V15, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  G1                0                 14
  G2                9                 74
  G3               13                 59
  G4                0                  1
  GX                0                  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"
D38V16, continuous
D38V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  21Q GAIN MUTATED                                             3
  21Q GAIN WILD-TYPE                                          18
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  21Q GAIN MUTATED                                        1
  21Q GAIN WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  21Q GAIN MUTATED                                                 0
  21Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  21Q GAIN MUTATED                4                  10
  21Q GAIN WILD-TYPE             32                  73
D38V18, multiclass
                                                 clus
vv                                                21Q GAIN 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                                                 4
  LIFELONG NON-SMOKER                                           10
                                                 clus
vv                                                21Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  32
  LIFELONG NON-SMOKER                                             73
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  21Q GAIN MUTATED             5        5             1        0
  21Q GAIN WILD-TYPE          12       32            10        5
D38V20, multiclass
               clus
vv              21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COMBINATION                  5                 12
  EXTERNAL                     5                 32
  EXTERNAL BEAM                1                 10
  INTERNAL                     0                  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"
D38V21, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    0  0
  21Q GAIN WILD-TYPE 11  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    0
  21Q GAIN WILD-TYPE   11    3
D38V22, continuous
D38V23, continuous
D38V24, continuous
D38V25, continuous
D38V26, continuous
D38V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  21Q GAIN MUTATED                                     0
  21Q GAIN WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  21Q GAIN MUTATED                                     0
  21Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  21Q GAIN MUTATED                         0                       0
  21Q GAIN WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  21Q GAIN MUTATED                         0
  21Q GAIN WILD-TYPE                       5
D38V28, multiclass
                    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                                                1
  21Q GAIN WILD-TYPE                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  21Q GAIN MUTATED                                                                                  14
  21Q GAIN WILD-TYPE                                                                                40
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  21Q GAIN MUTATED                                                                                              4
  21Q GAIN WILD-TYPE                                                                                           73
D38V29, multiclass
                                                                                              clus
vv                                                                                             21Q 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)                          14
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                4
                                                                                              clus
vv                                                                                             21Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            40
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 73
[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"
D38V30, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    7  6
  21Q GAIN WILD-TYPE 47 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7    6
  21Q GAIN WILD-TYPE   47   53
         clus
vv        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ABSENT                 7                 47
  PRESENT                6                 53
[1] 2 2
[1] FALSE
D38V31, continuous
D38V32, continuous
D38V33, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    6  5
  21Q GAIN WILD-TYPE 29 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      6    5
  21Q GAIN WILD-TYPE   29   76
                                          clus
vv                                         21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                5                 76
[1] 2 2
[1] FALSE
D38V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  21Q GAIN MUTATED       0                   11                   1
  21Q GAIN WILD-TYPE     3                  102                   4
D38V35, multiclass
                      clus
vv                     21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               11                102
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  21Q GAIN MUTATED              0           1          6
  21Q GAIN WILD-TYPE            8          39         34
D38V36, multiclass
              clus
vv             21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CURRENT USER                0                  8
  FORMER USER                 1                 39
  NEVER USED                  6                 34
[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, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    5  0
  21Q GAIN WILD-TYPE 68 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5    0
  21Q GAIN WILD-TYPE   68   14
         clus
vv        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ABSENT                 5                 68
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D38V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  21Q GAIN MUTATED     0    0   0    5    3  1   2    0    0   2   0  0  0
  21Q GAIN WILD-TYPE   2    1  22   46   18  2   4    6    8  11   2  1  7
D38V40, multiclass
      clus
vv     21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 0                 22
  T1B1                5                 46
  T1B2                3                 18
  T2                  1                  2
  T2A                 2                  4
  T2A1                0                  6
  T2A2                0                  8
  T2B                 2                 11
  T3B                 0                  2
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V41, continuous

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    18   1
  22Q GAIN WILD-TYPE 119  31
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                19                150 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 31 
$`22Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-C5-A1BJ TCGA-C5-A2LY TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UC 
       57.04       144.16        78.35       182.93        25.35        17.19 
TCGA-C5-A7UH TCGA-DS-A3LQ TCGA-EA-A1QS TCGA-EA-A5ZF TCGA-EK-A2RM TCGA-EK-A2RO 
       60.69        22.98         0.76        14.96         2.24         0.07 
TCGA-FU-A3NI TCGA-FU-A40J TCGA-JW-A5VI TCGA-LP-A4AU TCGA-MU-A51Y TCGA-MY-A5BE 
        1.45         1.35        16.64         0.10        13.87         0.07 
TCGA-PN-A8MA 
        2.96 

$`22Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        68.84        18.74        36.56 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       31.40        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       38.99        35.61         0.46         2.43        40.93         3.58 
TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 
       44.22        73.18        73.45        83.05       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CJ 
        0.82        52.01        18.02        17.85        20.42       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UI 
      134.33        15.48         9.67        73.41        85.55        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        9.34        13.61         2.73        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
        2.66       117.99       118.65        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05         1.18        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.81        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
       13.91         0.69        14.99        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       45.96         6.64         0.53         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A3GJ 
        0.03         0.36         1.18        23.70         0.10         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        4.47         6.12         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.66         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        26.56        36.36        14.43 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AW 
       19.33        20.48        15.58        10.06         5.13         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BF 
        0.07         0.82         0.03         5.42        29.72         4.34 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        3.72         3.45         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            182.93             177.04 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            14.960             13.265 
[1] "0.1 - 182.9 (15.0)" "0.0 - 177.0 (13.3)"
[1] "hr=" "4.4"
D39V2, continuous
                    vv
clus                 T1 T2+T3+T4
  22Q GAIN MUTATED    8        6
  22Q GAIN WILD-TYPE 89       33
D39V3, multiclass
          clus
vv         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                      8                 89
  T2+T3+T4                6                 33
[1] 2 2
[1] FALSE
D39V4, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    8  4
  22Q GAIN WILD-TYPE 79 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      8    4
  22Q GAIN WILD-TYPE   79   36
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                8                 79
  1                4                 36
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  22Q GAIN MUTATED    8  0  6
  22Q GAIN WILD-TYPE 64  3 59
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                8                 64
  M1                0                  3
  MX                6                 59
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED               0                               19
  22Q GAIN WILD-TYPE             2                              125
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  22Q GAIN MUTATED                                               0
  22Q GAIN WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  22Q GAIN MUTATED                                     1
  22Q GAIN WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  22Q GAIN MUTATED                                           0
  22Q GAIN WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  22Q GAIN MUTATED                                              0
  22Q GAIN WILD-TYPE                                            4
D39V6, multiclass
                                               clus
vv                                              22Q GAIN MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            19
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              22Q GAIN WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             125
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  17
  22Q GAIN WILD-TYPE  24 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   17
  22Q GAIN WILD-TYPE   24  132
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 3                 24
  YES               17                132
[1] 2 2
[1] FALSE
D39V8, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LZ         TCGA-C5-A2M2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UI         TCGA-C5-A7X8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-HM-A4S6         TCGA-HM-A6W2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-MU-A5YI         TCGA-MU-A8JM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741         TCGA-UC-A7PD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
D39V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  2     2
  22Q GAIN WILD-TYPE                                5    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED                           2
  22Q GAIN WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    13
  22Q GAIN WILD-TYPE                                         1   117
D39V10, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  5
  ASIAN                                                    2                 13
  BLACK OR AFRICAN AMERICAN                                2                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   13                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"
D39V11, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     2  13
  22Q GAIN WILD-TYPE   9 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2   13
  22Q GAIN WILD-TYPE    9  114
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               13                114
[1] 2 2
[1] FALSE
D39V12, continuous
D39V13, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    3  1
  22Q GAIN WILD-TYPE 45 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    1
  22Q GAIN WILD-TYPE   45   18
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  TUMOR FREE                3                 45
  WITH TUMOR                1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  22Q GAIN MUTATED         1      1       0            16       2
  22Q GAIN WILD-TYPE       0      9       6           131      10
D39V14, multiclass
               clus
vv              22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES               16                131
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  22Q GAIN MUTATED    1  9 10  0  0
  22Q GAIN WILD-TYPE 13 74 62  1  5
D39V15, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  G1                1                 13
  G2                9                 74
  G3               10                 62
  G4                0                  1
  GX                0                  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"
D39V16, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 23 
        TCGA-BI-A0VR         TCGA-C5-A1BL         TCGA-C5-A1BQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A7CM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-EX-A69M         TCGA-FU-A2QG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-HM-A3JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-MU-A5YI         TCGA-MU-A8JM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
D39V17, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LZ         TCGA-C5-A2M2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UI         TCGA-C5-A7X8 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A770         TCGA-HM-A4S6         TCGA-HM-A6W2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-MU-A5YI         TCGA-MU-A8JM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741         TCGA-UC-A7PD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  22Q GAIN MUTATED                                             1
  22Q GAIN WILD-TYPE                                          20
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  22Q GAIN MUTATED                                        1
  22Q GAIN WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  22Q GAIN MUTATED                                                 0
  22Q GAIN WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  22Q GAIN MUTATED                3                  10
  22Q GAIN WILD-TYPE             33                  73
D39V18, multiclass
                                                 clus
vv                                                22Q GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 3
  LIFELONG NON-SMOKER                                           10
                                                 clus
vv                                                22Q GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  33
  LIFELONG NON-SMOKER                                             73
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V19, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 46 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1BQ         TCGA-C5-A1M7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LZ         TCGA-C5-A2M2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A3HD         TCGA-C5-A3HF         TCGA-C5-A7CJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-DR-A0ZM         TCGA-DS-A5RQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A5XV         TCGA-FU-A770         TCGA-HM-A4S6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VK         TCGA-MU-A5YI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-UC-A7PD 
"22Q GAIN WILD-TYPE" 
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  22Q GAIN MUTATED             2        2             1        1
  22Q GAIN WILD-TYPE          15       35            10        4
D39V20, multiclass
               clus
vv              22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COMBINATION                  2                 15
  EXTERNAL                     2                 35
  EXTERNAL BEAM                1                 10
  INTERNAL                     1                  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"
D39V21, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    0  0
  22Q GAIN WILD-TYPE 11  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    0
  22Q GAIN WILD-TYPE   11    3
D39V22, continuous
D39V23, continuous
D39V24, continuous
D39V25, continuous
D39V26, continuous
D39V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  22Q GAIN MUTATED                                     1
  22Q GAIN WILD-TYPE                                   1
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  22Q GAIN MUTATED                                     0
  22Q GAIN WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  22Q GAIN MUTATED                         1                       0
  22Q GAIN WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  22Q GAIN MUTATED                         0
  22Q GAIN WILD-TYPE                       5
D39V28, multiclass
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 21 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A2LX         TCGA-DR-A0ZM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-EA-A50E         TCGA-EK-A2RN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A8JM         TCGA-UC-A7PD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
                    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                                                1
  22Q GAIN WILD-TYPE                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  22Q GAIN MUTATED                                                                                   3
  22Q GAIN WILD-TYPE                                                                                51
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  22Q GAIN MUTATED                                                                                             10
  22Q GAIN WILD-TYPE                                                                                           67
D39V29, multiclass
                                                                                              clus
vv                                                                                             22Q 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)                           3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               10
                                                                                              clus
vv                                                                                             22Q GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                9
  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)                 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"
D39V30, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    5  4
  22Q GAIN WILD-TYPE 49 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5    4
  22Q GAIN WILD-TYPE   49   55
         clus
vv        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ABSENT                 5                 49
  PRESENT                4                 55
[1] 2 2
[1] FALSE
D39V31, continuous
D39V32, continuous
D39V33, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  9
  22Q GAIN WILD-TYPE 31 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    9
  22Q GAIN WILD-TYPE   31   72
                                          clus
vv                                         22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                9                 72
[1] 2 2
[1] FALSE
D39V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  22Q GAIN MUTATED       0                   10                   1
  22Q GAIN WILD-TYPE     3                  103                   4
D39V35, multiclass
                      clus
vv                     22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               10                103
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  22Q GAIN MUTATED              0           6          2
  22Q GAIN WILD-TYPE            8          34         38
D39V36, multiclass
              clus
vv             22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CURRENT USER                0                  8
  FORMER USER                 6                 34
  NEVER USED                  2                 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"
D39V37, continuous
D39V38, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  0
  22Q GAIN WILD-TYPE 69 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    0
  22Q GAIN WILD-TYPE   69   14
         clus
vv        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ABSENT                 4                 69
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D39V39, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                  7 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MN 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MP         TCGA-HM-A3JK         TCGA-JW-A852 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-MU-A8JM 
"22Q GAIN WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  22Q GAIN MUTATED     0    0   2    6    0  1   0    2    0   2   1  0  0
  22Q GAIN WILD-TYPE   2    1  20   45   21  2   6    4    8  11   1  1  7
D39V40, multiclass
      clus
vv     22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 2                 20
  T1B1                6                 45
  T1B2                0                 21
  T2                  1                  2
  T2A                 0                  6
  T2A1                2                  4
  T2A2                0                  8
  T2B                 2                 11
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V41, continuous

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    21   2
  XQ GAIN WILD-TYPE 116  30
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               23               146 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                30 
$`XQ GAIN MUTATED`
TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MP 
      177.04        67.46        46.32        57.73        53.16         3.58 
TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A7CH TCGA-DS-A3LQ TCGA-EA-A3QD TCGA-EA-A5O9 
       73.45        83.05        25.35        22.98        13.05        13.91 
TCGA-EA-A5ZF TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RM TCGA-FU-A3NI 
       14.96        45.96         0.53         0.07         2.24         1.45 
TCGA-IR-A3LB TCGA-IR-A3LL TCGA-JW-A852 TCGA-LP-A5U3 TCGA-Q1-A5R3 
       66.81        36.36         5.13         0.82         5.85 

$`XQ GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       144.16       173.29        82.85         5.46        19.86 
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ 
       31.40        30.21        35.01        38.99        35.61         0.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ 
        2.43        40.93        44.22        73.18        78.35       100.14 
TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       38.43         0.82        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 
      182.93       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19        85.55        60.69        94.95         9.34        13.61 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
        2.73        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
      118.65        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
       12.36         1.74         1.32         0.82         0.62         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26        14.89         1.48         0.69        14.99 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RC 
       13.58        13.48        12.59         6.64         0.59         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO 
        0.03         0.36         1.18        23.70         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         4.47         6.12         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17         0.66         1.02         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         1.12        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         4.11       147.39       137.16 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-JW-A5VG 
      117.40        96.95        78.71        81.96        26.56        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-LP-A4AU 
       16.64        19.33        20.48        15.58        10.06         0.10 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.89         0.07        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT 
        0.07         4.34         2.96         3.72         3.45         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           177.04            182.93 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            22.98             12.74 
[1] "0.1 - 177.0 (23.0)" "0.0 - 182.9 (12.7)"
[1] "hr=" "3"  
D40V2, continuous
                   vv
clus                T1 T2+T3+T4
  XQ GAIN MUTATED   14        3
  XQ GAIN WILD-TYPE 83       36
D40V3, multiclass
          clus
vv         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                    14                83
  T2+T3+T4               3                36
[1] 2 2
[1] FALSE
D40V4, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    9  7
  XQ GAIN WILD-TYPE 78 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      9    7
  XQ GAIN WILD-TYPE   78   33
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               9                78
  1               7                33
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  XQ GAIN MUTATED    9  0  9
  XQ GAIN WILD-TYPE 63  3 56
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               9                63
  M1               0                 3
  MX               9                56
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED               0                               22
  XQ GAIN WILD-TYPE             2                              122
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  XQ GAIN MUTATED                                               0
  XQ GAIN WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  XQ GAIN MUTATED                                     2
  XQ GAIN WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  XQ GAIN MUTATED                                           0
  XQ GAIN WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  XQ GAIN MUTATED                                              0
  XQ GAIN WILD-TYPE                                            4
D40V6, multiclass
                                               clus
vv                                              XQ GAIN MUTATED
  ADENOSQUAMOUS                                               0
  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                                              XQ GAIN WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            122
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3  21
  XQ GAIN WILD-TYPE  24 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   21
  XQ GAIN WILD-TYPE   24  128
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                3                24
  YES              21               128
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     2
  XQ GAIN WILD-TYPE                                7    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED                           4
  XQ GAIN WILD-TYPE                        14
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           0    17
  XQ GAIN WILD-TYPE                                         1   113
D40V10, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   2                13
  BLACK OR AFRICAN AMERICAN                               4                14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  17               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"
D40V11, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  18
  XQ GAIN WILD-TYPE  10 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   18
  XQ GAIN WILD-TYPE   10  109
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              18               109
[1] 2 2
[1] FALSE
D40V12, continuous
D40V13, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   10  2
  XQ GAIN WILD-TYPE 38 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     10    2
  XQ GAIN WILD-TYPE   38   17
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  TUMOR FREE              10                38
  WITH TUMOR               2                17
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  XQ GAIN MUTATED         0      0       1            21       2
  XQ GAIN WILD-TYPE       1     10       5           126      10
D40V14, multiclass
               clus
vv              XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     1                 5
  UNITED STATES              21               126
  VIETNAM                     2                10
[1] 5 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                G1 G2 G3 G4 GX
  XQ GAIN MUTATED    1 12 11  0  0
  XQ GAIN WILD-TYPE 13 71 61  1  5
D40V15, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  G1               1                13
  G2              12                71
  G3              11                61
  G4               0                 1
  GX               0                 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"
D40V16, continuous
D40V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  XQ GAIN MUTATED                                             2
  XQ GAIN WILD-TYPE                                          19
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  XQ GAIN MUTATED                                        2
  XQ GAIN WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  XQ GAIN MUTATED                                                 0
  XQ GAIN WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  XQ GAIN MUTATED                5                  11
  XQ GAIN WILD-TYPE             31                  72
D40V18, multiclass
                                                 clus
vv                                                XQ GAIN MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                5
  LIFELONG NON-SMOKER                                          11
                                                 clus
vv                                                XQ GAIN WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 31
  LIFELONG NON-SMOKER                                            72
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  XQ GAIN MUTATED             3        5             1        0
  XQ GAIN WILD-TYPE          14       32            10        5
D40V20, multiclass
               clus
vv              XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COMBINATION                 3                14
  EXTERNAL                    5                32
  EXTERNAL BEAM               1                10
  INTERNAL                    0                 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"
D40V21, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    0  0
  XQ GAIN WILD-TYPE 11  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    0
  XQ GAIN WILD-TYPE   11    3
D40V22, continuous
D40V23, continuous
D40V24, continuous
D40V25, continuous
D40V26, continuous
D40V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  XQ GAIN MUTATED                                     0
  XQ GAIN WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  XQ GAIN MUTATED                                     0                       1
  XQ GAIN WILD-TYPE                                   6                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  XQ GAIN MUTATED                         0                       1
  XQ GAIN WILD-TYPE                       1                       4
D40V28, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                21 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-EA-A50E        TCGA-EK-A2RN        TCGA-EK-A2RO 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO        TCGA-HM-A4S6 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK        TCGA-MU-A8JM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-UC-A7PD 
"XQ GAIN WILD-TYPE" 
                   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                                                1
  XQ GAIN WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  XQ GAIN MUTATED                                                                                   7
  XQ GAIN WILD-TYPE                                                                                47
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  XQ GAIN MUTATED                                                                                             12
  XQ GAIN WILD-TYPE                                                                                           65
D40V29, multiclass
                                                                                              clus
vv                                                                                             XQ GAIN MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  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)              12
                                                                                              clus
vv                                                                                             XQ GAIN WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                65
[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"
D40V30, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    8  9
  XQ GAIN WILD-TYPE 46 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8    9
  XQ GAIN WILD-TYPE   46   50
         clus
vv        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ABSENT                8                46
  PRESENT               9                50
[1] 2 2
[1] FALSE
D40V31, continuous
D40V32, continuous
D40V33, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    7 10
  XQ GAIN WILD-TYPE 28 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      7   10
  XQ GAIN WILD-TYPE   28   71
                                          clus
vv                                         XQ GAIN MUTATED XQ GAIN WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   7                28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              10                71
[1] 2 2
[1] FALSE
D40V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  XQ GAIN MUTATED       1                   16                   0
  XQ GAIN WILD-TYPE     2                   97                   5
D40V35, multiclass
                      clus
vv                     XQ GAIN MUTATED XQ GAIN WILD-TYPE
  OTHER                              1                 2
  RADICAL HYSTERECTOMY              16                97
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  XQ GAIN MUTATED              0           7          5
  XQ GAIN WILD-TYPE            8          33         35
D40V36, multiclass
              clus
vv             XQ GAIN MUTATED XQ GAIN WILD-TYPE
  CURRENT USER               0                 8
  FORMER USER                7                33
  NEVER USED                 5                35
[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
D40V38, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   12  0
  XQ GAIN WILD-TYPE 61 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     12    0
  XQ GAIN WILD-TYPE   61   14
         clus
vv        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ABSENT               12                61
  PRESENT               0                14
[1] 2 2
[1] FALSE
D40V39, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                 7 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1MN        TCGA-EK-A2RO 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-MU-A51Y        TCGA-MU-A8JM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  XQ GAIN MUTATED     1    0   4    6    3  1   0    0    0   1   1  0  1
  XQ GAIN WILD-TYPE   1    1  18   45   18  2   6    6    8  12   1  1  6
D40V40, multiclass
      clus
vv     XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1A                1                 1
  T1A1               0                 1
  T1B                4                18
  T1B1               6                45
  T1B2               3                18
  T2                 1                 2
  T2A                0                 6
  T2A1               0                 6
  T2A2               0                 8
  T2B                1                12
  T3B                1                 1
  T4                 0                 1
  TX                 1                 6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V41, continuous

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED     4   1
  1P LOSS WILD-TYPE 133  31
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5               164 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                31 
$`1P LOSS MUTATED`
TCGA-C5-A1MI TCGA-C5-A2LT TCGA-C5-A7CH TCGA-C5-A7UH TCGA-DS-A0VN 
       35.61        73.18        25.35        60.69       118.65 

$`1P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       57.73        53.16        38.99         0.46         2.43        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         0.82        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 
      182.93       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       17.19        85.55        94.95         9.34        13.61         2.73 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       87.75        58.88        36.76         2.66       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18         7.33         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         0.26        14.89         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        6.64         0.53         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO 
        0.36         1.18        23.70         2.24         0.10         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.10         0.10         0.03        20.35         7.92         6.94 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         4.47         6.12         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36        14.43        16.64        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       15.58        10.06         5.13         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            25.35              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           118.65            182.93 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           60.690            12.935 
[1] "25.4 - 118.7 (60.7)" "0.0 - 182.9 (12.9)" 
[1] "hr=" "2.2"
D41V2, continuous
                   vv
clus                T1 T2+T3+T4
  1P LOSS MUTATED    3        0
  1P LOSS WILD-TYPE 94       39
D41V3, multiclass
          clus
vv         1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                     3                94
  T2+T3+T4               0                39
[1] 2 2
[1] FALSE
D41V4, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  1
  1P LOSS WILD-TYPE 85 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    1
  1P LOSS WILD-TYPE   85   39
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               2                85
  1               1                39
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED    3  0  0
  1P LOSS WILD-TYPE 69  3 65
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               3                69
  M1               0                 3
  MX               0                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED               0                                6
  1P LOSS WILD-TYPE             2                              138
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1P LOSS MUTATED                                               0
  1P LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1P LOSS MUTATED                                     1
  1P LOSS WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1P LOSS MUTATED                                           0
  1P LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1P LOSS MUTATED                                              0
  1P LOSS WILD-TYPE                                            4
D41V6, multiclass
                                               clus
vv                                              1P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            6
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              1P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            138
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3   4
  1P LOSS WILD-TYPE  24 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    4
  1P LOSS WILD-TYPE   24  145
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3                24
  YES               4               145
[1] 2 2
[1] FALSE
D41V8, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                51 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A2LS        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO        TCGA-C5-A7UE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-DR-A0ZM        TCGA-DS-A5RQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5        TCGA-FU-A2QG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HM-A4S6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A5YI        TCGA-MU-A8JM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D41V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     0
  1P LOSS WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED                           0
  1P LOSS WILD-TYPE                        18
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           0     7
  1P LOSS WILD-TYPE                                         1   123
D41V10, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   0                15
  BLACK OR AFRICAN AMERICAN                               0                18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   7               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"
D41V11, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1   5
  1P LOSS WILD-TYPE  10 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    5
  1P LOSS WILD-TYPE   10  122
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO               5               122
[1] 2 2
[1] FALSE
D41V12, continuous
D41V13, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  1
  1P LOSS WILD-TYPE 46 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    1
  1P LOSS WILD-TYPE   46   18
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  TUMOR FREE               2                46
  WITH TUMOR               1                18
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  1P LOSS MUTATED         0      0       0             7       0
  1P LOSS WILD-TYPE       1     10       6           140      12
D41V14, multiclass
               clus
vv              1P LOSS MUTATED 1P LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 6
  UNITED STATES               7               140
  VIETNAM                     0                12
[1] 5 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                G1 G2 G3 G4 GX
  1P LOSS MUTATED    0  5  2  0  0
  1P LOSS WILD-TYPE 14 78 70  1  5
D41V15, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  G1               0                14
  G2               5                78
  G3               2                70
  G4               0                 1
  GX               0                 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"
D41V16, continuous
D41V17, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                51 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A2LS        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO        TCGA-C5-A7UE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-DR-A0ZM        TCGA-DS-A5RQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5        TCGA-FU-A2QG 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HM-A4S6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A5YI        TCGA-MU-A8JM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  1P LOSS MUTATED                                             0
  1P LOSS WILD-TYPE                                          21
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  1P LOSS MUTATED                                        0
  1P LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  1P LOSS MUTATED                                                 0
  1P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1P LOSS MUTATED                2                   4
  1P LOSS WILD-TYPE             34                  79
D41V18, 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               0
  CURRENT SMOKER                                                2
  LIFELONG NON-SMOKER                                           4
                                                 clus
vv                                                1P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 34
  LIFELONG NON-SMOKER                                            79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V19, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                46 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A2LS        TCGA-C5-A2LV        TCGA-C5-A2LX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CL        TCGA-C5-A7CO        TCGA-C5-A7UE 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A7X8        TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-EA-A556 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HM-A4S6        TCGA-HM-A6W2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  1P LOSS MUTATED             1        0             2        1
  1P LOSS WILD-TYPE          16       37             9        4
D41V20, multiclass
               clus
vv              1P LOSS MUTATED 1P LOSS WILD-TYPE
  COMBINATION                 1                16
  EXTERNAL                    0                37
  EXTERNAL BEAM               2                 9
  INTERNAL                    1                 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"
D41V21, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    0  0
  1P LOSS WILD-TYPE 11  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0    0
  1P LOSS WILD-TYPE   11    3
D41V22, continuous
D41V23, continuous
D41V24, continuous
D41V25, continuous
D41V26, continuous
D41V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  1P LOSS MUTATED                                     0
  1P LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  1P LOSS MUTATED                                     0                       1
  1P LOSS WILD-TYPE                                   6                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1P LOSS MUTATED                         0                       0
  1P LOSS WILD-TYPE                       1                       5
D41V28, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                22 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A3LQ        TCGA-EA-A50E        TCGA-EK-A2RN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-UC-A7PD 
"1P LOSS WILD-TYPE" "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                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1P LOSS MUTATED                                                                                   1
  1P LOSS WILD-TYPE                                                                                53
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1P LOSS MUTATED                                                                                              2
  1P LOSS WILD-TYPE                                                                                           75
D41V29, 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)                          1
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               2
                                                                                              clus
vv                                                                                             1P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                75
[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"
D41V30, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  1
  1P LOSS WILD-TYPE 51 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    1
  1P LOSS WILD-TYPE   51   58
         clus
vv        1P LOSS MUTATED 1P LOSS WILD-TYPE
  ABSENT                3                51
  PRESENT               1                58
[1] 2 2
[1] FALSE
D41V31, continuous
D41V32, continuous
D41V33, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  0
  1P LOSS WILD-TYPE 32 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    0
  1P LOSS WILD-TYPE   32   81
                                          clus
vv                                         1P LOSS MUTATED 1P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   3                32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               0                81
[1] 2 2
[1] FALSE
D41V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  1P LOSS MUTATED       0                    3                   0
  1P LOSS WILD-TYPE     3                  110                   5
D41V35, multiclass
                      clus
vv                     1P LOSS MUTATED 1P LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY               3               110
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1P LOSS MUTATED              1           2          0
  1P LOSS WILD-TYPE            7          38         40
D41V36, multiclass
              clus
vv             1P LOSS MUTATED 1P LOSS WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                2                38
  NEVER USED                 0                40
[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
D41V38, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    4  0
  1P LOSS WILD-TYPE 69 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    0
  1P LOSS WILD-TYPE   69   14
         clus
vv        1P LOSS MUTATED 1P LOSS WILD-TYPE
  ABSENT                4                69
  PRESENT               0                14
[1] 2 2
[1] FALSE
D41V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  1P LOSS MUTATED     0    0   1    1    1  0   0    0    0   0   0  0  0
  1P LOSS WILD-TYPE   2    1  21   50   20  3   6    6    8  13   2  1  7
D41V40, multiclass
      clus
vv     1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                1                21
  T1B1               1                50
  T1B2               1                20
  T2                 0                 3
  T2A                0                 6
  T2A1               0                 6
  T2A2               0                 8
  T2B                0                13
  T3B                0                 2
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V41, continuous

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     5   2
  1Q LOSS WILD-TYPE 132  30
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               162 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                30 
$`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        25.35        60.69       118.65 
TCGA-HM-A3JJ 
       21.67 

$`1Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       57.73        53.16        38.99         0.46         2.43        40.93 
TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
        3.58        44.22        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 
        0.82        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48         9.67        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL 
       85.55        94.95         9.34        13.61         2.73        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18         7.33         8.28         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
        1.35         1.35        14.50         1.81        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        0.26        14.89         1.48        13.91         0.69        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.96        13.58        13.48        12.59        45.96         6.64 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.53         0.59         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        23.70         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        4.47         6.12         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.66         1.02         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        3.52         1.35         1.32         1.97         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         4.11       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       14.43        16.64        19.33        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
        5.13         0.10         0.89         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        3.72         3.45         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            21.67              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           118.65            182.93 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            60.69             12.74 
[1] "21.7 - 118.7 (60.7)" "0.0 - 182.9 (12.7)" 
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                T1 T2+T3+T4
  1Q LOSS MUTATED    5        0
  1Q LOSS WILD-TYPE 92       39
D42V3, multiclass
          clus
vv         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1                     5                92
  T2+T3+T4               0                39
[1] 2 2
[1] FALSE
D42V4, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    2  3
  1Q LOSS WILD-TYPE 85 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    3
  1Q LOSS WILD-TYPE   85   37
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               2                85
  1               3                37
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1Q LOSS MUTATED    3  0  2
  1Q LOSS WILD-TYPE 69  3 63
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               3                69
  M1               0                 3
  MX               2                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED               0                                7
  1Q LOSS WILD-TYPE             2                              137
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  1Q LOSS MUTATED                                               0
  1Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  1Q LOSS MUTATED                                     0
  1Q LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  1Q LOSS MUTATED                                           0
  1Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  1Q LOSS MUTATED                                              0
  1Q LOSS WILD-TYPE                                            4
D42V6, multiclass
                                               clus
vv                                              1Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            7
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              1Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            137
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     4   3
  1Q LOSS WILD-TYPE  23 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4    3
  1Q LOSS WILD-TYPE   23  146
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                4                23
  YES               3               146
[1] 2 2
[1] FALSE
D42V8, continuous
D42V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     0
  1Q LOSS WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED                           2
  1Q LOSS WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0     5
  1Q LOSS WILD-TYPE                                         1   125
D42V10, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   0                15
  BLACK OR AFRICAN AMERICAN                               2                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   5               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"
D42V11, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   7
  1Q LOSS WILD-TYPE  11 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    7
  1Q LOSS WILD-TYPE   11  120
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               7               120
[1] 2 2
[1] FALSE
D42V12, continuous
D42V13, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  2
  1Q LOSS WILD-TYPE 45 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    2
  1Q LOSS WILD-TYPE   45   17
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  TUMOR FREE               3                45
  WITH TUMOR               2                17
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  1Q LOSS MUTATED         0      0       0             7       0
  1Q LOSS WILD-TYPE       1     10       6           140      12
D42V14, multiclass
               clus
vv              1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      0                10
  UKRAINE                     0                 6
  UNITED STATES               7               140
  VIETNAM                     0                12
[1] 5 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                G1 G2 G3 G4 GX
  1Q LOSS MUTATED    0  3  4  0  0
  1Q LOSS WILD-TYPE 14 80 68  1  5
D42V15, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  G1               0                14
  G2               3                80
  G3               4                68
  G4               0                 1
  GX               0                 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"
D42V16, continuous
D42V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  1Q LOSS MUTATED                                             0
  1Q LOSS WILD-TYPE                                          21
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  1Q LOSS MUTATED                                        0
  1Q LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  1Q LOSS MUTATED                                                 0
  1Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  1Q LOSS MUTATED                3                   3
  1Q LOSS WILD-TYPE             33                  80
D42V18, 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               0
  CURRENT SMOKER                                                3
  LIFELONG NON-SMOKER                                           3
                                                 clus
vv                                                1Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 33
  LIFELONG NON-SMOKER                                            80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  1Q LOSS MUTATED             1        0             3        1
  1Q LOSS WILD-TYPE          16       37             8        4
D42V20, multiclass
               clus
vv              1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COMBINATION                 1                16
  EXTERNAL                    0                37
  EXTERNAL BEAM               3                 8
  INTERNAL                    1                 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"
D42V21, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    1  0
  1Q LOSS WILD-TYPE 10  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    0
  1Q LOSS WILD-TYPE   10    3
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CGY               1                10
  GY                0                 3
[1] 2 2
[1] FALSE
D42V22, continuous
D42V23, continuous
D42V24, continuous
D42V25, continuous
D42V26, continuous
D42V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  1Q LOSS MUTATED                                     0
  1Q LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  1Q LOSS MUTATED                                     0                       1
  1Q LOSS WILD-TYPE                                   6                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  1Q LOSS MUTATED                         0                       0
  1Q LOSS WILD-TYPE                       1                       5
D42V28, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                22 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A3LQ        TCGA-EA-A50E        TCGA-EK-A2RN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-UC-A7PD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   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                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  1Q LOSS MUTATED                                                                                   0
  1Q LOSS WILD-TYPE                                                                                54
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  1Q LOSS MUTATED                                                                                              4
  1Q LOSS WILD-TYPE                                                                                           73
D42V29, 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)                          0
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               4
                                                                                              clus
vv                                                                                             1Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                73
[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"
D42V30, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  2
  1Q LOSS WILD-TYPE 51 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    2
  1Q LOSS WILD-TYPE   51   57
         clus
vv        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ABSENT                3                51
  PRESENT               2                57
[1] 2 2
[1] FALSE
D42V31, continuous
D42V32, continuous
D42V33, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  2
  1Q LOSS WILD-TYPE 32 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    2
  1Q LOSS WILD-TYPE   32   79
                                          clus
vv                                         1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   3                32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               2                79
[1] 2 2
[1] FALSE
D42V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  1Q LOSS MUTATED       0                    5                   0
  1Q LOSS WILD-TYPE     3                  108                   5
D42V35, multiclass
                      clus
vv                     1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY               5               108
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  1Q LOSS MUTATED              1           3          1
  1Q LOSS WILD-TYPE            7          37         39
D42V36, multiclass
              clus
vv             1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                3                37
  NEVER USED                 1                39
[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
D42V38, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    4  0
  1Q LOSS WILD-TYPE 69 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      4    0
  1Q LOSS WILD-TYPE   69   14
         clus
vv        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ABSENT                4                69
  PRESENT               0                14
[1] 2 2
[1] FALSE
D42V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  1Q LOSS MUTATED     0    0   2    2    1  0   0    0    0   0   0  0  0
  1Q LOSS WILD-TYPE   2    1  20   49   20  3   6    6    8  13   2  1  7
D42V40, multiclass
      clus
vv     1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                2                20
  T1B1               2                49
  T1B2               1                20
  T2                 0                 3
  T2A                0                 6
  T2A1               0                 6
  T2A2               0                 8
  T2B                0                13
  T3B                0                 2
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V41, continuous

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     9   1
  2P LOSS WILD-TYPE 128  31
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               159 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                31 
$`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       182.93       118.65         1.32 
TCGA-EA-A3QD TCGA-EK-A2PG TCGA-EK-A2RN TCGA-Q1-A5R1 
       13.05         0.53         0.10         3.72 

$`2P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        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-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP 
       53.16        35.61         0.46         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-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
       38.43         0.82        52.01        17.85        20.42        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48         9.67        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 
       85.55        60.69        94.95         9.34        13.61         2.73 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ 
       87.75        58.88        36.76         2.66       117.99        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18         7.33         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        1.74         0.82         0.62         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35        14.50         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 
       13.58        13.48        12.59        45.96         6.64         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.24         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70         4.47         6.12         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU 
       19.33        20.48        15.58        10.06         5.13         0.10 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.89         0.07         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       29.72         0.07         4.34         2.96         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.10              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           182.93            177.04 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           15.535            13.580 
[1] "0.1 - 182.9 (15.5)" "0.0 - 177.0 (13.6)"
[1] "hr=" "2.8"
D43V2, continuous
                   vv
clus                T1 T2+T3+T4
  2P LOSS MUTATED    6        2
  2P LOSS WILD-TYPE 91       37
D43V3, multiclass
          clus
vv         2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1                     6                91
  T2+T3+T4               2                37
[1] 2 2
[1] FALSE
D43V4, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    6  2
  2P LOSS WILD-TYPE 81 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    2
  2P LOSS WILD-TYPE   81   38
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               6                81
  1               2                38
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2P LOSS MUTATED    5  0  3
  2P LOSS WILD-TYPE 67  3 62
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               5                67
  M1               0                 3
  MX               3                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED               0                                9
  2P LOSS WILD-TYPE             2                              135
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2P LOSS MUTATED                                               0
  2P LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2P LOSS MUTATED                                     0
  2P LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2P LOSS MUTATED                                           0
  2P LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2P LOSS MUTATED                                              1
  2P LOSS WILD-TYPE                                            3
D43V6, multiclass
                                               clus
vv                                              2P 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                                              2P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            135
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2   8
  2P LOSS WILD-TYPE  25 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    8
  2P LOSS WILD-TYPE   25  141
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                2                25
  YES               8               141
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                52 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MN 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-DR-A0ZM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-HM-A6W2        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-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A5YI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED                           1
  2P LOSS WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           0     9
  2P LOSS WILD-TYPE                                         1   121
D43V10, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   0                15
  BLACK OR AFRICAN AMERICAN                               1                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               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"
D43V11, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0   8
  2P LOSS WILD-TYPE  11 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    8
  2P LOSS WILD-TYPE   11  119
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               8               119
[1] 2 2
[1] FALSE
D43V12, continuous
D43V13, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    3  1
  2P LOSS WILD-TYPE 45 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    1
  2P LOSS WILD-TYPE   45   18
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  TUMOR FREE               3                45
  WITH TUMOR               1                18
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  2P LOSS MUTATED         0      1       0             9       0
  2P LOSS WILD-TYPE       1      9       6           138      12
D43V14, multiclass
               clus
vv              2P LOSS MUTATED 2P LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     0                 6
  UNITED STATES               9               138
  VIETNAM                     0                12
[1] 5 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                G1 G2 G3 G4 GX
  2P LOSS MUTATED    0  5  5  0  0
  2P LOSS WILD-TYPE 14 78 67  1  5
D43V15, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  G1               0                14
  G2               5                78
  G3               5                67
  G4               0                 1
  GX               0                 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"
D43V16, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                24 
       TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL        TCGA-C5-A1BQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A2M2        TCGA-C5-A3HD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-DS-A3LQ        TCGA-EX-A69M 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-HM-A3JK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D43V17, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                52 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MN 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-DR-A0ZM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-HM-A6W2        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-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A5YI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2P LOSS MUTATED                                             0
  2P LOSS WILD-TYPE                                          21
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  2P LOSS MUTATED                                        1
  2P LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  2P LOSS MUTATED                                                 0
  2P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2P LOSS MUTATED                1                   6
  2P LOSS WILD-TYPE             35                  77
D43V18, multiclass
                                                 clus
vv                                                2P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                1
  LIFELONG NON-SMOKER                                           6
                                                 clus
vv                                                2P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 35
  LIFELONG NON-SMOKER                                            77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  2P LOSS MUTATED             1        2             1        0
  2P LOSS WILD-TYPE          16       35            10        5
D43V20, multiclass
               clus
vv              2P LOSS MUTATED 2P LOSS WILD-TYPE
  COMBINATION                 1                16
  EXTERNAL                    2                35
  EXTERNAL BEAM               1                10
  INTERNAL                    0                 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"
D43V21, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    0  0
  2P LOSS WILD-TYPE 11  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    0
  2P LOSS WILD-TYPE   11    3
D43V22, continuous
D43V23, continuous
D43V24, continuous
D43V25, continuous
D43V26, continuous
D43V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  2P LOSS MUTATED                                     0
  2P LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  2P LOSS MUTATED                                     0                       2
  2P LOSS WILD-TYPE                                   6                       7
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2P LOSS MUTATED                         0                       0
  2P LOSS WILD-TYPE                       1                       5
D43V28, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                21 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A3LQ        TCGA-EA-A50E        TCGA-EK-A2RO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO        TCGA-HM-A4S6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK        TCGA-MU-A8JM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-UC-A7PD 
"2P LOSS WILD-TYPE" 
                   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                                                0
  2P LOSS WILD-TYPE                                             10
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2P LOSS MUTATED                                                                                   5
  2P LOSS WILD-TYPE                                                                                49
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2P LOSS MUTATED                                                                                              3
  2P LOSS WILD-TYPE                                                                                           74
D43V29, multiclass
                                                                                              clus
vv                                                                                             2P 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)                          5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               3
                                                                                              clus
vv                                                                                             2P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                              10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                74
[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"
D43V30, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    4  2
  2P LOSS WILD-TYPE 50 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4    2
  2P LOSS WILD-TYPE   50   57
         clus
vv        2P LOSS MUTATED 2P LOSS WILD-TYPE
  ABSENT                4                50
  PRESENT               2                57
[1] 2 2
[1] FALSE
D43V31, continuous
D43V32, continuous
D43V33, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    4  5
  2P LOSS WILD-TYPE 31 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4    5
  2P LOSS WILD-TYPE   31   76
                                          clus
vv                                         2P LOSS MUTATED 2P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   4                31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               5                76
[1] 2 2
[1] FALSE
D43V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  2P LOSS MUTATED       0                    8                   0
  2P LOSS WILD-TYPE     3                  105                   5
D43V35, multiclass
                      clus
vv                     2P LOSS MUTATED 2P LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY               8               105
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2P LOSS MUTATED              1           2          2
  2P LOSS WILD-TYPE            7          38         38
D43V36, multiclass
              clus
vv             2P LOSS MUTATED 2P LOSS WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                2                38
  NEVER USED                 2                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"
D43V37, continuous
D43V38, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    3  0
  2P LOSS WILD-TYPE 70 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    0
  2P LOSS WILD-TYPE   70   14
         clus
vv        2P LOSS MUTATED 2P LOSS WILD-TYPE
  ABSENT                3                70
  PRESENT               0                14
[1] 2 2
[1] FALSE
D43V39, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                 8 
       TCGA-C5-A1BN        TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-EK-A2RO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  2P LOSS MUTATED     0    0   1    3    2  0   1    0    0   1   0  0  0
  2P LOSS WILD-TYPE   2    1  21   48   19  3   5    6    8  12   2  1  7
D43V40, multiclass
      clus
vv     2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                1                21
  T1B1               3                48
  T1B2               2                19
  T2                 0                 3
  T2A                1                 5
  T2A1               0                 6
  T2A2               0                 8
  T2B                1                12
  T3B                0                 2
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V41, continuous

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    14   2
  2Q LOSS WILD-TYPE 123  30
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               153 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                30 
$`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       182.93 
TCGA-DS-A0VN TCGA-EA-A3HR TCGA-EA-A3QD TCGA-EA-A44S TCGA-EK-A2PG TCGA-EK-A2RN 
      118.65         1.32        13.05        12.66         0.53         0.10 
TCGA-EX-A69L TCGA-HM-A3JJ TCGA-MY-A5BF TCGA-Q1-A5R1 
        4.47        21.67         4.34         3.72 

$`2Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ 
       49.48        23.67        11.44        68.84        18.74       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI 
       31.40        46.32        35.01        57.73        53.16        35.61 
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         0.82 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       52.01        17.85        20.42        25.35       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48         9.67        73.41        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       94.95         9.34        13.61         2.73        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       117.99        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS 
        7.33         8.28         0.76        12.36         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
        0.62         1.18        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        1.81        12.82         0.26        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
        0.69        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       45.96         6.64         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.36         1.18        23.70         2.24         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.12         1.22        23.84         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK 
        1.35         1.32         1.97         1.12        25.41        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        26.56        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       16.64        19.33        20.48        15.58        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        0.10         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        5.42        29.72         0.07         2.96         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.10              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           182.93            177.04 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           15.535            13.580 
[1] "0.1 - 182.9 (15.5)" "0.0 - 177.0 (13.6)"
[1] "hr=" "1.8"
D44V2, continuous
                   vv
clus                T1 T2+T3+T4
  2Q LOSS MUTATED   10        4
  2Q LOSS WILD-TYPE 87       35
D44V3, multiclass
          clus
vv         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1                    10                87
  T2+T3+T4               4                35
[1] 2 2
[1] FALSE
D44V4, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    9  5
  2Q LOSS WILD-TYPE 78 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9    5
  2Q LOSS WILD-TYPE   78   35
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               9                78
  1               5                35
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2Q LOSS MUTATED    8  0  6
  2Q LOSS WILD-TYPE 64  3 59
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               8                64
  M1               0                 3
  MX               6                59
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED               0                               15
  2Q LOSS WILD-TYPE             2                              129
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  2Q LOSS MUTATED                                               0
  2Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  2Q LOSS MUTATED                                     0
  2Q LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  2Q LOSS MUTATED                                           0
  2Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  2Q LOSS MUTATED                                              1
  2Q LOSS WILD-TYPE                                            3
D44V6, multiclass
                                               clus
vv                                              2Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           15
  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                                              2Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            129
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     5  11
  2Q LOSS WILD-TYPE  22 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5   11
  2Q LOSS WILD-TYPE   22  138
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                5                22
  YES              11               138
[1] 2 2
[1] FALSE
D44V8, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                51 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MN        TCGA-C5-A2LS 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO        TCGA-C5-A7UE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-DR-A0ZM        TCGA-DS-A5RQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5        TCGA-FU-A2QG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HM-A4S6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A5YI        TCGA-MU-A8JM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D44V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     1
  2Q LOSS WILD-TYPE                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED                           2
  2Q LOSS WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           0    13
  2Q LOSS WILD-TYPE                                         1   117
D44V10, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   1                14
  BLACK OR AFRICAN AMERICAN                               2                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  13               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"
D44V11, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  14
  2Q LOSS WILD-TYPE  11 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   14
  2Q LOSS WILD-TYPE   11  113
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              14               113
[1] 2 2
[1] FALSE
D44V12, continuous
D44V13, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    4  2
  2Q LOSS WILD-TYPE 44 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4    2
  2Q LOSS WILD-TYPE   44   17
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  TUMOR FREE               4                44
  WITH TUMOR               2                17
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  2Q LOSS MUTATED         0      1       1            14       0
  2Q LOSS WILD-TYPE       1      9       5           133      12
D44V14, multiclass
               clus
vv              2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     1                 5
  UNITED STATES              14               133
  VIETNAM                     0                12
[1] 5 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                G1 G2 G3 G4 GX
  2Q LOSS MUTATED    1  8  7  0  0
  2Q LOSS WILD-TYPE 13 75 65  1  5
D44V15, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  G1               1                13
  G2               8                75
  G3               7                65
  G4               0                 1
  GX               0                 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"
D44V16, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                24 
       TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL        TCGA-C5-A1BQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A2M2        TCGA-C5-A3HD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-DS-A3LQ        TCGA-EX-A69M 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-HM-A3JK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D44V17, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                51 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A1MN        TCGA-C5-A2LS 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A2M2        TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO        TCGA-C5-A7UE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-DR-A0ZM        TCGA-DS-A5RQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DS-A7WF        TCGA-EA-A556        TCGA-EX-A1H5        TCGA-FU-A2QG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HM-A4S6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A5YI        TCGA-MU-A8JM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  2Q LOSS MUTATED                                             0
  2Q LOSS WILD-TYPE                                          21
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  2Q LOSS MUTATED                                        1
  2Q LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  2Q LOSS MUTATED                                                 0
  2Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  2Q LOSS MUTATED                2                  10
  2Q LOSS WILD-TYPE             34                  73
D44V18, multiclass
                                                 clus
vv                                                2Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                2
  LIFELONG NON-SMOKER                                          10
                                                 clus
vv                                                2Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 34
  LIFELONG NON-SMOKER                                            73
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V19, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                47 
       TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL        TCGA-C5-A1BN 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME        TCGA-C5-A1MF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A1MI        TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CL        TCGA-C5-A7CO 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7X8        TCGA-DR-A0ZM        TCGA-DS-A5RQ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EA-A556        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HM-A4S6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A5YI        TCGA-MU-A8JM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  2Q LOSS MUTATED             2        3             3        0
  2Q LOSS WILD-TYPE          15       34             8        5
D44V20, multiclass
               clus
vv              2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COMBINATION                 2                15
  EXTERNAL                    3                34
  EXTERNAL BEAM               3                 8
  INTERNAL                    0                 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"
D44V21, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    1  0
  2Q LOSS WILD-TYPE 10  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    0
  2Q LOSS WILD-TYPE   10    3
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CGY               1                10
  GY                0                 3
[1] 2 2
[1] FALSE
D44V22, continuous
D44V23, continuous
D44V24, continuous
D44V25, continuous
D44V26, continuous
D44V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  2Q LOSS MUTATED                                     0
  2Q LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  2Q LOSS MUTATED                                     0                       2
  2Q LOSS WILD-TYPE                                   6                       7
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  2Q LOSS MUTATED                         0                       0
  2Q LOSS WILD-TYPE                       1                       5
D44V28, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                21 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A3LQ        TCGA-EA-A50E        TCGA-EK-A2RO 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO        TCGA-HM-A4S6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK        TCGA-MU-A8JM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-UC-A7PD 
"2Q LOSS WILD-TYPE" 
                   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                                                0
  2Q LOSS WILD-TYPE                                             10
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  2Q LOSS MUTATED                                                                                   6
  2Q LOSS WILD-TYPE                                                                                48
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  2Q LOSS MUTATED                                                                                              7
  2Q LOSS WILD-TYPE                                                                                           70
D44V29, multiclass
                                                                                              clus
vv                                                                                             2Q 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)                          6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               7
                                                                                              clus
vv                                                                                             2Q LOSS WILD-TYPE
  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)                           48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                70
[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"
D44V30, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    5  5
  2Q LOSS WILD-TYPE 49 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    5
  2Q LOSS WILD-TYPE   49   54
         clus
vv        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ABSENT                5                49
  PRESENT               5                54
[1] 2 2
[1] FALSE
D44V31, continuous
D44V32, continuous
D44V33, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    4  8
  2Q LOSS WILD-TYPE 31 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4    8
  2Q LOSS WILD-TYPE   31   73
                                          clus
vv                                         2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   4                31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               8                73
[1] 2 2
[1] FALSE
D44V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  2Q LOSS MUTATED       1                   11                   0
  2Q LOSS WILD-TYPE     2                  102                   5
D44V35, multiclass
                      clus
vv                     2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  OTHER                              1                 2
  RADICAL HYSTERECTOMY              11               102
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  2Q LOSS MUTATED              1           4          5
  2Q LOSS WILD-TYPE            7          36         35
D44V36, multiclass
              clus
vv             2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                4                36
  NEVER USED                 5                35
[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
D44V38, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    5  0
  2Q LOSS WILD-TYPE 68 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    0
  2Q LOSS WILD-TYPE   68   14
         clus
vv        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ABSENT                5                68
  PRESENT               0                14
[1] 2 2
[1] FALSE
D44V39, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                 8 
       TCGA-C5-A1BN        TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-EK-A2RO 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  2Q LOSS MUTATED     0    0   3    5    2  0   1    0    2   1   0  0  0
  2Q LOSS WILD-TYPE   2    1  19   46   19  3   5    6    6  12   2  1  7
D44V40, multiclass
      clus
vv     2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                3                19
  T1B1               5                46
  T1B2               2                19
  T2                 0                 3
  T2A                1                 5
  T2A1               0                 6
  T2A2               2                 6
  T2B                1                12
  T3B                0                 2
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V41, continuous

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    32   9
  3P LOSS WILD-TYPE 105  23
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               41               128 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                23 
$`3P LOSS MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BM 
       49.48        23.67        11.44        18.74        36.56        82.85 
TCGA-C5-A1BN TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LX TCGA-C5-A7CH TCGA-C5-A7CO 
        5.46        35.61        40.93        83.05        25.35        73.41 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VK 
       85.55        94.95        13.61         2.73        87.75        36.76 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-EA-A3HS TCGA-EA-A3QE TCGA-EA-A411 
      117.99       118.65        16.83         0.82         1.18         1.35 
TCGA-EA-A44S TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB 
       12.66        14.99        13.58         6.64         0.59         0.07 
TCGA-EK-A2RE TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3YQ TCGA-FU-A5XV 
        0.36        20.35        23.84         0.66         3.52         1.97 
TCGA-IR-A3L7 TCGA-JW-A5VI TCGA-MU-A5YI TCGA-Q1-A5R2 TCGA-RA-A741 
      147.39        16.64         0.03         3.45         3.88 

$`3P LOSS WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BQ 
       57.04        68.84       144.16       177.04       173.29        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS 
       53.16        38.99         0.46         2.43         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         0.82 
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       182.93       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 
      134.33        15.48         9.67        17.19        60.69         9.34 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
       58.88         2.66        22.98        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A3QD 
        0.76        12.36         1.74         1.32         0.62        13.05 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E 
       14.50         1.35        14.50         1.81        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A78R 
       14.89         1.48        13.91         0.69        14.96        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RJ 
       12.59        45.96         0.53         4.04         0.03         1.18 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
       23.70         2.24         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        1.22         0.92         2.17         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA 
        1.48         0.82         1.35         1.32         1.12        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB 
       21.67        20.78        14.93         4.11       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       14.43        19.33        20.48        15.58        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM 
        0.10         0.89         0.07         0.82        13.87         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 
       29.72         0.07         4.34         2.96         3.72         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.03              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           147.39            182.93 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           16.640            12.705 
[1] "0.0 - 147.4 (16.6)" "0.0 - 182.9 (12.7)"
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                T1 T2+T3+T4
  3P LOSS MUTATED   22        9
  3P LOSS WILD-TYPE 75       30
D45V3, multiclass
          clus
vv         3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                    22                75
  T2+T3+T4               9                30
[1] 2 2
[1] FALSE
D45V4, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   15 15
  3P LOSS WILD-TYPE 72 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     15   15
  3P LOSS WILD-TYPE   72   25
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              15                72
  1              15                25
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3P LOSS MUTATED   17  0 16
  3P LOSS WILD-TYPE 55  3 49
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              17                55
  M1               0                 3
  MX              16                49
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED               0                               41
  3P LOSS WILD-TYPE             2                              103
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3P LOSS MUTATED                                               0
  3P LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3P LOSS MUTATED                                     0
  3P LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3P LOSS MUTATED                                           0
  3P LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3P LOSS MUTATED                                              1
  3P LOSS WILD-TYPE                                            3
D45V6, multiclass
                                               clus
vv                                              3P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           41
  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                                              3P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            103
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    10  32
  3P LOSS WILD-TYPE  17 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10   32
  3P LOSS WILD-TYPE   17  117
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               10                17
  YES              32               117
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  1     3
  3P LOSS WILD-TYPE                                6    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED                           6
  3P LOSS WILD-TYPE                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           0    32
  3P LOSS WILD-TYPE                                         1    98
D45V10, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   3                12
  BLACK OR AFRICAN AMERICAN                               6                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  32                98
[1] 5 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
  3P LOSS MUTATED    1 34
  3P LOSS WILD-TYPE 10 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   34
  3P LOSS WILD-TYPE   10   93
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              34                93
[1] 2 2
[1] FALSE
D45V12, continuous
D45V13, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   13  4
  3P LOSS WILD-TYPE 35 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     13    4
  3P LOSS WILD-TYPE   35   15
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  TUMOR FREE              13                35
  WITH TUMOR               4                15
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  3P LOSS MUTATED         0      3       1            36       2
  3P LOSS WILD-TYPE       1      7       5           111      10
D45V14, multiclass
               clus
vv              3P LOSS MUTATED 3P LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      3                 7
  UKRAINE                     1                 5
  UNITED STATES              36               111
  VIETNAM                     2                10
[1] 5 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                G1 G2 G3 G4 GX
  3P LOSS MUTATED    3 17 20  0  1
  3P LOSS WILD-TYPE 11 66 52  1  4
D45V15, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  G1               3                11
  G2              17                66
  G3              20                52
  G4               0                 1
  GX               1                 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"
D45V16, continuous
D45V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3P LOSS MUTATED                                             5
  3P LOSS WILD-TYPE                                          16
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  3P LOSS MUTATED                                        2
  3P LOSS WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  3P LOSS MUTATED                                                 0
  3P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3P LOSS MUTATED               16                  13
  3P LOSS WILD-TYPE             20                  70
D45V18, multiclass
                                                 clus
vv                                                3P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   5
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               16
  LIFELONG NON-SMOKER                                          13
                                                 clus
vv                                                3P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 20
  LIFELONG NON-SMOKER                                            70
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  3P LOSS MUTATED             7        9             3        2
  3P LOSS WILD-TYPE          10       28             8        3
D45V20, multiclass
               clus
vv              3P LOSS MUTATED 3P LOSS WILD-TYPE
  COMBINATION                 7                10
  EXTERNAL                    9                28
  EXTERNAL BEAM               3                 8
  INTERNAL                    2                 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"
D45V21, binary
                   cls
clus                0 1
  3P LOSS MUTATED   3 1
  3P LOSS WILD-TYPE 8 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    1
  3P LOSS WILD-TYPE    8    2
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  CGY               3                 8
  GY                1                 2
[1] 2 2
[1] FALSE
D45V22, continuous
D45V23, continuous
D45V24, continuous
D45V25, continuous
D45V26, continuous
D45V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  3P LOSS MUTATED                                     0
  3P LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  3P LOSS MUTATED                                     3                       2
  3P LOSS WILD-TYPE                                   3                       7
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3P LOSS MUTATED                         0                       3
  3P LOSS WILD-TYPE                       1                       2
D45V28, multiclass
                                     clus
vv                                    3P LOSS MUTATED 3P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               3                 3
  OTHER LOCATION, SPECIFY                           2                 7
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           3                 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)
  3P LOSS MUTATED                                               0
  3P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  3P LOSS MUTATED                                                3
  3P LOSS WILD-TYPE                                              7
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3P LOSS MUTATED                                                                                  12
  3P LOSS WILD-TYPE                                                                                42
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3P LOSS MUTATED                                                                                             17
  3P LOSS WILD-TYPE                                                                                           60
D45V29, multiclass
                                                                                              clus
vv                                                                                             3P 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)                         12
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              17
                                                                                              clus
vv                                                                                             3P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           42
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                60
[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"
D45V30, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    8 19
  3P LOSS WILD-TYPE 46 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      8   19
  3P LOSS WILD-TYPE   46   40
         clus
vv        3P LOSS MUTATED 3P LOSS WILD-TYPE
  ABSENT                8                46
  PRESENT              19                40
[1] 2 2
[1] FALSE
D45V31, continuous
D45V32, continuous
D45V33, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   11 21
  3P LOSS WILD-TYPE 24 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     11   21
  3P LOSS WILD-TYPE   24   60
                                          clus
vv                                         3P LOSS MUTATED 3P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  11                24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              21                60
[1] 2 2
[1] FALSE
D45V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  3P LOSS MUTATED       0                   28                   0
  3P LOSS WILD-TYPE     3                   85                   5
D45V35, multiclass
                      clus
vv                     3P LOSS MUTATED 3P LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              28                85
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3P LOSS MUTATED              1          12          7
  3P LOSS WILD-TYPE            7          28         33
D45V36, multiclass
              clus
vv             3P LOSS MUTATED 3P LOSS WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER               12                28
  NEVER USED                 7                33
[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
D45V38, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   17  4
  3P LOSS WILD-TYPE 56 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     17    4
  3P LOSS WILD-TYPE   56   10
         clus
vv        3P LOSS MUTATED 3P LOSS WILD-TYPE
  ABSENT               17                56
  PRESENT               4                10
[1] 2 2
[1] FALSE
D45V39, continuous
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                 7 
       TCGA-C5-A1MH        TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-HM-A3JK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  3P LOSS MUTATED     0    1   4   14    3  2   1    1    2   3   0  0  2
  3P LOSS WILD-TYPE   2    0  18   37   18  1   5    5    6  10   2  1  5
D45V40, multiclass
      clus
vv     3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1A                0                 2
  T1A1               1                 0
  T1B                4                18
  T1B1              14                37
  T1B2               3                18
  T2                 2                 1
  T2A                1                 5
  T2A1               1                 5
  T2A2               2                 6
  T2B                3                10
  T3B                0                 2
  T4                 0                 1
  TX                 2                 5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V41, continuous

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     4   1
  3Q LOSS WILD-TYPE 133  31
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5               164 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                31 
$`3Q LOSS MUTATED`
TCGA-C5-A7CH TCGA-C5-A7X5 TCGA-EA-A411 TCGA-EK-A2RJ TCGA-MU-A5YI 
       25.35        13.61         1.35         1.18         0.03 

$`3Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43         0.82        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       182.93       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
        9.67        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        9.34         2.73        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 
        0.62        13.05         1.18        14.50         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.81        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91         0.69        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB 
       12.59        45.96         6.64         0.53         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN 
        4.04         0.03         0.36        23.70         2.24         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70         4.47         6.12         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        25.41        21.67        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.07         0.82        13.87         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.03              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            25.35            182.93 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            1.350            13.725 
[1] "0.0 - 25.4 (1.4)"   "0.0 - 182.9 (13.7)"
[1] "hr=" "3.3"
D46V2, continuous
                   vv
clus                T1 T2+T3+T4
  3Q LOSS MUTATED    3        0
  3Q LOSS WILD-TYPE 94       39
D46V3, multiclass
          clus
vv         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1                     3                94
  T2+T3+T4               0                39
[1] 2 2
[1] FALSE
D46V4, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  0
  3Q LOSS WILD-TYPE 85 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    0
  3Q LOSS WILD-TYPE   85   40
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               2                85
  1               0                40
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3Q LOSS MUTATED    1  0  2
  3Q LOSS WILD-TYPE 71  3 63
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               1                71
  M1               0                 3
  MX               2                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED               0                                6
  3Q LOSS WILD-TYPE             2                              138
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  3Q LOSS MUTATED                                               0
  3Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  3Q LOSS MUTATED                                     0
  3Q LOSS WILD-TYPE                                  20
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  3Q LOSS MUTATED                                           0
  3Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  3Q LOSS MUTATED                                              0
  3Q LOSS WILD-TYPE                                            4
D46V6, multiclass
                                               clus
vv                                              3Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                            6
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              3Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            138
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   6
  3Q LOSS WILD-TYPE  27 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    6
  3Q LOSS WILD-TYPE   27  143
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                27
  YES               6               143
[1] 2 2
[1] FALSE
D46V8, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                52 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7UI        TCGA-C5-A7X8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A770        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D46V9, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2               105 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-BI-A20A        TCGA-C5-A0TN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BE        TCGA-C5-A1BF        TCGA-C5-A1BK        TCGA-C5-A1BL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BM        TCGA-C5-A1M5        TCGA-C5-A1M7        TCGA-C5-A1M8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1M9        TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MJ        TCGA-C5-A1MP        TCGA-C5-A2LT        TCGA-C5-A2LV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2M1        TCGA-C5-A3HF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HL        TCGA-C5-A7CJ        TCGA-C5-A7UC        TCGA-C5-A7UE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A43B        TCGA-EA-A44S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A4BA        TCGA-EA-A50E        TCGA-EA-A556        TCGA-EA-A5FO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A5O9        TCGA-EA-A6QX        TCGA-EK-A2RO        TCGA-EK-A3GK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1        TCGA-EX-A69L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A69M        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A40J        TCGA-FU-A57G        TCGA-FU-A5XV        TCGA-FU-A770 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB        TCGA-IR-A3LC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-LP-A4AX        TCGA-MU-A51Y        TCGA-MU-A8JM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MY-A5BD        TCGA-MY-A5BF        TCGA-Q1-A5R1        TCGA-Q1-A6DV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Q1-A73P        TCGA-R2-A69V        TCGA-RA-A741        TCGA-UC-A7PD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UC-A7PF 
"3Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED                           2
  3Q LOSS WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           0     4
  3Q LOSS WILD-TYPE                                         1   126
D46V10, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   0                15
  BLACK OR AFRICAN AMERICAN                               2                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   4               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"
D46V11, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   5
  3Q LOSS WILD-TYPE  11 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    5
  3Q LOSS WILD-TYPE   11  122
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO               5               122
[1] 2 2
[1] FALSE
D46V12, continuous
D46V13, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    0  0
  3Q LOSS WILD-TYPE 48 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    0
  3Q LOSS WILD-TYPE   48   19
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  3Q LOSS MUTATED         0      1       0             5       0
  3Q LOSS WILD-TYPE       1      9       6           142      12
D46V14, multiclass
               clus
vv              3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     0                 6
  UNITED STATES               5               142
  VIETNAM                     0                12
[1] 5 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                G1 G2 G3 G4 GX
  3Q LOSS MUTATED    0  3  2  0  0
  3Q LOSS WILD-TYPE 14 80 70  1  5
D46V15, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  G1               0                14
  G2               3                80
  G3               2                70
  G4               0                 1
  GX               0                 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"
D46V16, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                24 
       TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL        TCGA-C5-A1BQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A2M2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-DS-A3LQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A69M        TCGA-FU-A2QG        TCGA-FU-A3TX        TCGA-FU-A3WB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-HM-A4S6        TCGA-IR-A3L7        TCGA-IR-A3LB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D46V17, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                52 
       TCGA-BI-A0VR        TCGA-C5-A1BF        TCGA-C5-A1BI        TCGA-C5-A1BJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7UI        TCGA-C5-A7X8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-EA-A556 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A770        TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  3Q LOSS MUTATED                                             0
  3Q LOSS WILD-TYPE                                          21
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  3Q LOSS MUTATED                                        1
  3Q LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  3Q LOSS MUTATED                                                 0
  3Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  3Q LOSS MUTATED                0                   2
  3Q LOSS WILD-TYPE             36                  81
D46V18, multiclass
                                                 clus
vv                                                3Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                0
  LIFELONG NON-SMOKER                                           2
                                                 clus
vv                                                3Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 36
  LIFELONG NON-SMOKER                                            81
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V19, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                47 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MI        TCGA-C5-A2LS        TCGA-C5-A2LT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7X8        TCGA-DR-A0ZM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-EA-A556        TCGA-EX-A1H5        TCGA-FU-A2QG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3TX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-FU-A5XV        TCGA-FU-A770 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-JW-A5VI        TCGA-JW-A5VK        TCGA-MU-A8JM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Q1-A6DW        TCGA-RA-A741        TCGA-UC-A7PD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  3Q LOSS MUTATED             0        1             0        0
  3Q LOSS WILD-TYPE          17       36            11        5
D46V20, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                69 
       TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BF        TCGA-C5-A1BI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BL        TCGA-C5-A1BM        TCGA-C5-A1BN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6        TCGA-C5-A1M8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1M9        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LT        TCGA-C5-A2LX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LY        TCGA-C5-A2LZ        TCGA-C5-A3HE        TCGA-C5-A3HF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HL        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7X8        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-DS-A5RQ        TCGA-DS-A7WH        TCGA-DS-A7WI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3QD        TCGA-EA-A3Y4        TCGA-EA-A44S        TCGA-EA-A4BA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A5O9        TCGA-EX-A3L1        TCGA-EX-A449        TCGA-FU-A23L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6        TCGA-HM-A6W2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB        TCGA-IR-A3LC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-JW-A5VG        TCGA-JW-A5VI        TCGA-PN-A8MA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Q1-A5R2        TCGA-Q1-A5R3        TCGA-R2-A69V        TCGA-RA-A741 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UC-A7PD 
"3Q LOSS WILD-TYPE" 
D46V21, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    0  0
  3Q LOSS WILD-TYPE 11  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    0
  3Q LOSS WILD-TYPE   11    3
D46V22, continuous
D46V23, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                91 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BE        TCGA-C5-A1BI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI        TCGA-C5-A1MJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-C5-A2LS 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HE        TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-C5-A7X8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A44S        TCGA-EA-A556 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A5O9        TCGA-EX-A449        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3TQ        TCGA-FU-A770 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK        TCGA-IR-A3L7        TCGA-IR-A3LC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-JW-A5VG        TCGA-JW-A5VI        TCGA-JW-A5VJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-JW-A5VL        TCGA-JW-A69B        TCGA-JW-A852 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D46V24, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2               103 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BE        TCGA-C5-A1BF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BM        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1M6        TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MJ        TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A1MP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LY        TCGA-C5-A2LZ        TCGA-C5-A2M1        TCGA-C5-A2M2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HE        TCGA-C5-A3HF        TCGA-C5-A3HL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7CG        TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7CO        TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7UI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7X3        TCGA-C5-A7X8        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH        TCGA-DS-A7WI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A44S        TCGA-EA-A556 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A5O9        TCGA-EA-A5ZD        TCGA-EK-A2IP        TCGA-EK-A2RK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A69L        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3HZ        TCGA-FU-A3TQ        TCGA-FU-A3YQ        TCGA-FU-A57G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JK        TCGA-HM-A4S6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LC        TCGA-IR-A3LF        TCGA-IR-A3LH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LI        TCGA-IR-A3LK        TCGA-IR-A3LL        TCGA-JW-A5VG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A5VL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-JW-A69B        TCGA-JW-A852        TCGA-MU-A8JM        TCGA-PN-A8MA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D46V25, continuous
D46V26, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                98 
       TCGA-BI-A0VS        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI        TCGA-C5-A1MJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-C5-A2LS 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HE        TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-C5-A7X8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3QE        TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A44S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A4BA        TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EA-A6QX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EK-A2RN        TCGA-EX-A1H6        TCGA-EX-A449        TCGA-FU-A2QG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3TQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JJ        TCGA-HM-A3JK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LC        TCGA-IR-A3LF        TCGA-IR-A3LH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LI        TCGA-IR-A3LK        TCGA-IR-A3LL        TCGA-JW-A5VG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-JW-A5VI        TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A5VL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-JW-A69B        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-RA-A741 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UC-A7PD        TCGA-UC-A7PF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D46V27, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                92 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BE        TCGA-C5-A1BI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL        TCGA-C5-A1BM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5        TCGA-C5-A1M6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI        TCGA-C5-A1MJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-C5-A2LS 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HE        TCGA-C5-A3HF        TCGA-C5-A3HL        TCGA-C5-A7CG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7CJ        TCGA-C5-A7CK        TCGA-C5-A7CL        TCGA-C5-A7CO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7UH        TCGA-C5-A7X3        TCGA-C5-A7X8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZL        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A44S        TCGA-EA-A556 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A5O9        TCGA-EX-A69M        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3TQ        TCGA-FU-A5XV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A770        TCGA-HG-A2PA        TCGA-HM-A3JK        TCGA-IR-A3L7 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LC        TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LK        TCGA-IR-A3LL        TCGA-JW-A5VG        TCGA-JW-A5VI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A5VL        TCGA-JW-A69B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-RA-A741        TCGA-UC-A7PD        TCGA-UC-A7PF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  3Q LOSS MUTATED                                     0
  3Q LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  3Q LOSS MUTATED                                     0                       0
  3Q LOSS WILD-TYPE                                   6                       9
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  3Q LOSS MUTATED                         0                       0
  3Q LOSS WILD-TYPE                       1                       5
D46V28, 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                                             10
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  3Q LOSS MUTATED                                                                                   2
  3Q LOSS WILD-TYPE                                                                                52
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  3Q LOSS MUTATED                                                                                              0
  3Q LOSS WILD-TYPE                                                                                           77
D46V29, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2               141 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A0TN        TCGA-C5-A1BE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BK        TCGA-C5-A1BL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BM        TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1M6        TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A1MI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MJ        TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A1MP 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LT        TCGA-C5-A2LV        TCGA-C5-A2LX        TCGA-C5-A2LY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LZ        TCGA-C5-A2M1        TCGA-C5-A2M2        TCGA-C5-A3HF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HL        TCGA-C5-A7CO        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3QE        TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A439 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EA-A44S        TCGA-EA-A4BA        TCGA-EA-A50E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5FO        TCGA-EA-A5O9        TCGA-EA-A5ZD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A5ZE        TCGA-EA-A5ZF        TCGA-EA-A6QX        TCGA-EA-A78R 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EK-A2GZ        TCGA-EK-A2H0        TCGA-EK-A2PG        TCGA-EK-A2PM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EK-A2R7        TCGA-EK-A2RD        TCGA-EK-A2RE        TCGA-EK-A2RK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EK-A2RN        TCGA-EK-A2RO        TCGA-EK-A3GM        TCGA-EX-A1H5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A1H6        TCGA-EX-A3L1        TCGA-EX-A449        TCGA-EX-A69L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A69M        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3YQ        TCGA-FU-A40J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A57G        TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HG-A2PA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6        TCGA-HM-A6W2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB        TCGA-IR-A3LC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-JW-A5VG        TCGA-JW-A5VI        TCGA-JW-A5VJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-JW-A5VL        TCGA-JW-A69B        TCGA-JW-A852 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-LP-A4AU        TCGA-LP-A4AW        TCGA-LP-A4AX        TCGA-LP-A5U3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MU-A51Y        TCGA-MY-A5BD        TCGA-MY-A5BE        TCGA-MY-A5BF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-PN-A8MA        TCGA-Q1-A5R1        TCGA-Q1-A5R2        TCGA-Q1-A5R3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Q1-A6DT        TCGA-Q1-A6DV        TCGA-Q1-A6DW        TCGA-Q1-A73P 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Q1-A73R        TCGA-R2-A69V        TCGA-RA-A741        TCGA-UC-A7PD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UC-A7PF 
"3Q LOSS WILD-TYPE" 
D46V30, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  2
  3Q LOSS WILD-TYPE 53 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    2
  3Q LOSS WILD-TYPE   53   57
         clus
vv        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ABSENT                1                53
  PRESENT               2                57
[1] 2 2
[1] FALSE
D46V31, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2               105 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-BI-A20A        TCGA-C5-A0TN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BE        TCGA-C5-A1BF        TCGA-C5-A1BK        TCGA-C5-A1BL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1BM        TCGA-C5-A1M5        TCGA-C5-A1M7        TCGA-C5-A1M8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1M9        TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A1MI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MJ        TCGA-C5-A1MP        TCGA-C5-A2LT        TCGA-C5-A2LV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2M1        TCGA-C5-A3HF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HL        TCGA-C5-A7CJ        TCGA-C5-A7UC        TCGA-C5-A7UE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7UI        TCGA-C5-A7X8        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-DS-A5RQ        TCGA-DS-A7WF        TCGA-DS-A7WH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A7WI        TCGA-EA-A1QS        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A3QD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3Y4        TCGA-EA-A410        TCGA-EA-A43B        TCGA-EA-A44S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A4BA        TCGA-EA-A50E        TCGA-EA-A556        TCGA-EA-A5FO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A5O9        TCGA-EA-A6QX        TCGA-EK-A2RO        TCGA-EK-A3GK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1        TCGA-EX-A69L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A69M        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A40J        TCGA-FU-A57G        TCGA-FU-A5XV        TCGA-FU-A770 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JJ        TCGA-HM-A3JK        TCGA-HM-A4S6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LA        TCGA-IR-A3LB        TCGA-IR-A3LC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LF        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LL        TCGA-LP-A4AX        TCGA-MU-A51Y        TCGA-MU-A8JM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MY-A5BD        TCGA-MY-A5BF        TCGA-Q1-A5R1        TCGA-Q1-A6DV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Q1-A73P        TCGA-R2-A69V        TCGA-RA-A741        TCGA-UC-A7PD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UC-A7PF 
"3Q LOSS WILD-TYPE" 
D46V32, continuous
D46V33, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  4
  3Q LOSS WILD-TYPE 33 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    4
  3Q LOSS WILD-TYPE   33   77
                                          clus
vv                                         3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   2                33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               4                77
[1] 2 2
[1] FALSE
D46V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  3Q LOSS MUTATED       0                    3                   0
  3Q LOSS WILD-TYPE     3                  110                   5
D46V35, multiclass
                      clus
vv                     3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY               3               110
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  3Q LOSS MUTATED              0           1          0
  3Q LOSS WILD-TYPE            8          39         40
D46V36, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                87 
       TCGA-C5-A1BI        TCGA-C5-A1BL        TCGA-C5-A1BN        TCGA-C5-A1M6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1M7        TCGA-C5-A1M8        TCGA-C5-A1M9        TCGA-C5-A1ME 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MN        TCGA-C5-A2LT        TCGA-C5-A2LV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LY        TCGA-C5-A2M1        TCGA-C5-A2M2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A3HD        TCGA-C5-A3HL        TCGA-C5-A7CG        TCGA-C5-A7UH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-C5-A7X3        TCGA-DR-A0ZL        TCGA-DR-A0ZM        TCGA-DS-A0VK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A3LQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DS-A7WF        TCGA-DS-A7WH        TCGA-DS-A7WI        TCGA-EA-A1QS 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR        TCGA-EA-A3HS 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A3HT        TCGA-EA-A3QD        TCGA-EA-A3QE        TCGA-EA-A410 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EA-A44S        TCGA-EA-A4BA        TCGA-EA-A50E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EA-A556        TCGA-EA-A5O9        TCGA-EA-A5ZE        TCGA-EA-A5ZF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EK-A2R7        TCGA-EK-A3GK        TCGA-EX-A1H5        TCGA-EX-A1H6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-EX-A69L        TCGA-EX-A69M        TCGA-FU-A2QG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FU-A57G        TCGA-FU-A770        TCGA-HM-A3JJ        TCGA-HM-A3JK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-HM-A6W2        TCGA-IR-A3L7        TCGA-IR-A3LA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LB        TCGA-IR-A3LC        TCGA-IR-A3LF        TCGA-IR-A3LH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IR-A3LI        TCGA-IR-A3LK        TCGA-JW-A5VG        TCGA-JW-A5VI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-JW-A5VJ        TCGA-JW-A5VK        TCGA-JW-A69B        TCGA-LP-A5U3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-PN-A8MA        TCGA-Q1-A5R1        TCGA-Q1-A5R2        TCGA-Q1-A5R3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Q1-A6DV        TCGA-Q1-A73P        TCGA-UC-A7PD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D46V37, continuous
D46V38, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  0
  3Q LOSS WILD-TYPE 72 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    0
  3Q LOSS WILD-TYPE   72   14
         clus
vv        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ABSENT                1                72
  PRESENT               0                14
[1] 2 2
[1] FALSE
D46V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  3Q LOSS MUTATED     0    1   0    1    1  0   0    0    0   0   0  0  0
  3Q LOSS WILD-TYPE   2    0  22   50   20  3   6    6    8  13   2  1  7
D46V40, multiclass
      clus
vv     3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1A                0                 2
  T1A1               1                 0
  T1B                0                22
  T1B1               1                50
  T1B2               1                20
  T2                 0                 3
  T2A                0                 6
  T2A1               0                 6
  T2A2               0                 8
  T2B                0                13
  T3B                0                 2
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V41, continuous

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   53 15
  4P LOSS WILD-TYPE 84 17
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               68               101 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               15                17 
$`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-A1MP TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A3HE 
        3.58        73.18        73.45        83.05       100.14        18.02 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
      134.33        15.48         9.67        73.41        17.19        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL 
       94.95         9.34         2.73        87.75        36.76         2.66 
TCGA-DS-A0VN TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3Y4 
      118.65        16.83        12.36         1.32         0.82        14.50 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A78R TCGA-EK-A2GZ 
        1.35        14.50         1.81        12.66        13.48        12.59 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN 
        0.53         0.59         0.03         1.18         2.24         0.10 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI 
        0.10        20.35         6.94        23.84         0.66         1.45 
TCGA-FU-A5XV TCGA-HM-A3JJ TCGA-IR-A3LH TCGA-JW-A5VK TCGA-LP-A4AU TCGA-LP-A4AW 
        1.97        21.67        78.71        20.48         0.10         0.89 
TCGA-LP-A4AX TCGA-MU-A8JM TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         5.42         4.34         2.96         3.45         5.85 
TCGA-Q1-A6DT TCGA-UC-A7PD 
        3.39        11.67 

$`4P LOSS WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
       57.04        23.67        18.74        82.85        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK 
       46.32        30.21        57.73        38.99         0.46         2.43 
TCGA-C5-A1MN TCGA-C5-A2LS TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       40.93        44.22        78.35        38.43         0.82        52.01 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7UE 
       17.85        20.42       182.93        25.35       101.82        85.55 
TCGA-C5-A7X5 TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A7WF TCGA-DS-A7WH 
       13.61        58.88       117.99        22.98        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        8.28         0.76         1.74         0.62        13.05         1.18 
TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
        1.35        12.82         0.26        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2H0 TCGA-EK-A2IP 
        0.69        14.99        14.96        13.58        45.96         6.64 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.07         4.04         0.36        23.70         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        0.03         7.92        14.70         4.47         6.12         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.92         2.17         1.02         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK 
        3.52         1.35         1.32         1.12        25.41        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       96.95        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A5U3 TCGA-MU-A51Y 
       19.33        15.58        10.06         5.13         0.82        13.87 
TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-Q1-A5R1 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        0.03        29.72         0.07         3.72         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        93.99 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.03              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           177.04            182.93 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           12.625            13.870 
[1] "0.0 - 177.0 (12.6)" "0.0 - 182.9 (13.9)"
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                T1 T2+T3+T4
  4P LOSS MUTATED   38       15
  4P LOSS WILD-TYPE 59       24
D47V3, multiclass
          clus
vv         4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                    38                59
  T2+T3+T4              15                24
[1] 2 2
[1] FALSE
D47V4, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   30 21
  4P LOSS WILD-TYPE 57 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     30   21
  4P LOSS WILD-TYPE   57   19
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              30                57
  1              21                19
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED   30  0 26
  4P LOSS WILD-TYPE 42  3 39
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              30                42
  M1               0                 3
  MX              26                39
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED               0                               67
  4P LOSS WILD-TYPE             2                               77
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4P LOSS MUTATED                                               1
  4P LOSS WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4P LOSS MUTATED                                     2
  4P LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4P LOSS MUTATED                                           0
  4P LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4P LOSS MUTATED                                              1
  4P LOSS WILD-TYPE                                            3
D47V6, multiclass
                                               clus
vv                                              4P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           67
  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                                              4P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                             77
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D47V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   15 56
  4P LOSS WILD-TYPE 12 93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     15   56
  4P LOSS WILD-TYPE   12   93
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               15                12
  YES              56                93
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  2     6
  4P LOSS WILD-TYPE                                5     9
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED                          12
  4P LOSS WILD-TYPE                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           0    51
  4P LOSS WILD-TYPE                                         1    79
D47V10, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 5
  ASIAN                                                   6                 9
  BLACK OR AFRICAN AMERICAN                              12                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  51                79
[1] 5 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
  4P LOSS MUTATED    1 57
  4P LOSS WILD-TYPE 10 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   57
  4P LOSS WILD-TYPE   10   70
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              57                70
[1] 2 2
[1] FALSE
D47V12, continuous
D47V13, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   18  8
  4P LOSS WILD-TYPE 30 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     18    8
  4P LOSS WILD-TYPE   30   11
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  TUMOR FREE              18                30
  WITH TUMOR               8                11
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  4P LOSS MUTATED         1      4       3            58       5
  4P LOSS WILD-TYPE       0      6       3            89       7
D47V14, multiclass
               clus
vv              4P LOSS MUTATED 4P LOSS WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      4                 6
  UKRAINE                     3                 3
  UNITED STATES              58                89
  VIETNAM                     5                 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                G1 G2 G3 G4 GX
  4P LOSS MUTATED    3 32 34  1  1
  4P LOSS WILD-TYPE 11 51 38  0  4
D47V15, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  G1               3                11
  G2              32                51
  G3              34                38
  G4               1                 0
  GX               1                 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"
D47V16, continuous
D47V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4P LOSS MUTATED                                             8
  4P LOSS WILD-TYPE                                          13
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  4P LOSS MUTATED                                        3
  4P LOSS WILD-TYPE                                      5
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  4P LOSS MUTATED                                                 1
  4P LOSS WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4P LOSS MUTATED               16                  29
  4P LOSS WILD-TYPE             20                  54
D47V18, multiclass
                                                 clus
vv                                                4P 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                                               16
  LIFELONG NON-SMOKER                                          29
                                                 clus
vv                                                4P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    13
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 20
  LIFELONG NON-SMOKER                                            54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  4P LOSS MUTATED             9       15             6        4
  4P LOSS WILD-TYPE           8       22             5        1
D47V20, multiclass
               clus
vv              4P LOSS MUTATED 4P LOSS WILD-TYPE
  COMBINATION                 9                 8
  EXTERNAL                   15                22
  EXTERNAL BEAM               6                 5
  INTERNAL                    4                 1
[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"
D47V21, binary
                   cls
clus                0 1
  4P LOSS MUTATED   7 1
  4P LOSS WILD-TYPE 4 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      7    1
  4P LOSS WILD-TYPE    4    2
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  CGY               7                 4
  GY                1                 2
[1] 2 2
[1] FALSE
D47V22, continuous
D47V23, continuous
D47V24, continuous
D47V25, continuous
D47V26, continuous
D47V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  4P LOSS MUTATED                                     0
  4P LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  4P LOSS MUTATED                                     3                       5
  4P LOSS WILD-TYPE                                   3                       4
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4P LOSS MUTATED                         0                       3
  4P LOSS WILD-TYPE                       1                       2
D47V28, multiclass
                                     clus
vv                                    4P LOSS MUTATED 4P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               3                 3
  OTHER LOCATION, SPECIFY                           5                 4
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           3                 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)
  4P LOSS MUTATED                                               0
  4P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  4P LOSS MUTATED                                                4
  4P LOSS WILD-TYPE                                              6
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4P LOSS MUTATED                                                                                  23
  4P LOSS WILD-TYPE                                                                                31
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4P LOSS MUTATED                                                                                             30
  4P LOSS WILD-TYPE                                                                                           47
D47V29, multiclass
                                                                                              clus
vv                                                                                             4P 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)                         23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              30
                                                                                              clus
vv                                                                                             4P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               6
  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)                47
[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"
D47V30, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   17 27
  4P LOSS WILD-TYPE 37 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     17   27
  4P LOSS WILD-TYPE   37   32
         clus
vv        4P LOSS MUTATED 4P LOSS WILD-TYPE
  ABSENT               17                37
  PRESENT              27                32
[1] 2 2
[1] FALSE
D47V31, continuous
D47V32, continuous
D47V33, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   18 33
  4P LOSS WILD-TYPE 17 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     18   33
  4P LOSS WILD-TYPE   17   48
                                          clus
vv                                         4P LOSS MUTATED 4P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  18                17
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              33                48
[1] 2 2
[1] FALSE
D47V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  4P LOSS MUTATED       1                   46                   3
  4P LOSS WILD-TYPE     2                   67                   2
D47V35, multiclass
                      clus
vv                     4P LOSS MUTATED 4P LOSS WILD-TYPE
  OTHER                              1                 2
  RADICAL HYSTERECTOMY              46                67
  SIMPLE HYSTERECTOMY                3                 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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4P LOSS MUTATED              4          15         14
  4P LOSS WILD-TYPE            4          25         26
D47V36, multiclass
              clus
vv             4P LOSS MUTATED 4P LOSS WILD-TYPE
  CURRENT USER               4                 4
  FORMER USER               15                25
  NEVER USED                14                26
[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
D47V38, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   25  4
  4P LOSS WILD-TYPE 48 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     25    4
  4P LOSS WILD-TYPE   48   10
         clus
vv        4P LOSS MUTATED 4P LOSS WILD-TYPE
  ABSENT               25                48
  PRESENT               4                10
[1] 2 2
[1] FALSE
D47V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  4P LOSS MUTATED     1    0  13   16    8  2   2    4    2   4   1  0  3
  4P LOSS WILD-TYPE   1    1   9   35   13  1   4    2    6   9   1  1  4
D47V40, multiclass
      clus
vv     4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1A                1                 1
  T1A1               0                 1
  T1B               13                 9
  T1B1              16                35
  T1B2               8                13
  T2                 2                 1
  T2A                2                 4
  T2A1               4                 2
  T2A2               2                 6
  T2B                4                 9
  T3B                1                 1
  T4                 0                 1
  TX                 3                 4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V41, continuous

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    33  11
  4Q LOSS WILD-TYPE 104  21
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               44               125 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               11                21 
$`4Q LOSS MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M9 
       49.48        23.67        11.44         5.46        31.40        35.01 
TCGA-C5-A1MI TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A3HE TCGA-C5-A7CL 
       35.61        73.18        73.45        83.05        18.02        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-C5-A7X5 
        9.67        73.41        17.19        60.69         9.34        13.61 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 
        2.73        87.75         0.76        12.36         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A556 TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG 
        1.81        14.89        13.48        12.59        45.96         0.53 
TCGA-EK-A2R7 TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-EX-A3L1 
        0.59         1.18         2.24         0.10        20.35         6.94 
TCGA-FU-A3NI TCGA-FU-A5XV TCGA-HM-A3JJ TCGA-JW-A5VK TCGA-LP-A4AU TCGA-PN-A8MA 
        1.45         1.97        21.67        20.48         0.10         2.96 
TCGA-Q1-A5R2 TCGA-UC-A7PD 
        3.45        11.67 

$`4Q LOSS WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       57.04        68.84        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29        82.85        19.86        67.46        46.32        30.21 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       57.73        53.16        38.99         0.46         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         0.82 
TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ 
       52.01        17.85        20.42       182.93        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7UE TCGA-C5-A7UI TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
      134.33        85.55        94.95        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
        8.28         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.18        14.50         1.35        12.66        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL 
        6.64         0.07         4.04         0.03         0.36        23.70 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 
        0.07         0.10         0.10         0.03         7.92        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        4.47         6.12         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.66         1.02         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 
        1.35         1.32         1.12        25.41        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AW TCGA-LP-A4AX 
       19.33        15.58        10.06         5.13         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34         3.72         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        93.99 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.10              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            87.75            182.93 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           13.035            13.870 
[1] "0.1 - 87.8 (13.0)"  "0.0 - 182.9 (13.9)"
[1] "hr=" "2.1"
D48V2, continuous
                   vv
clus                T1 T2+T3+T4
  4Q LOSS MUTATED   22       10
  4Q LOSS WILD-TYPE 75       29
D48V3, multiclass
          clus
vv         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                    22                75
  T2+T3+T4              10                29
[1] 2 2
[1] FALSE
D48V4, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   16 14
  4Q LOSS WILD-TYPE 71 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     16   14
  4Q LOSS WILD-TYPE   71   26
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              16                71
  1              14                26
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED   21  0 12
  4Q LOSS WILD-TYPE 51  3 53
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              21                51
  M1               0                 3
  MX              12                53
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED               0                               43
  4Q LOSS WILD-TYPE             2                              101
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  4Q LOSS MUTATED                                               1
  4Q LOSS WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  4Q LOSS MUTATED                                     2
  4Q LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  4Q LOSS MUTATED                                           1
  4Q LOSS WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  4Q LOSS MUTATED                                              1
  4Q LOSS WILD-TYPE                                            3
D48V6, multiclass
                                               clus
vv                                              4Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           43
  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                                              4Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            101
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     9  39
  4Q LOSS WILD-TYPE  18 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9   39
  4Q LOSS WILD-TYPE   18  110
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                9                18
  YES              39               110
[1] 2 2
[1] FALSE
D48V8, continuous
D48V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  1     4
  4Q LOSS WILD-TYPE                                6    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED                           9
  4Q LOSS WILD-TYPE                         9
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           0    34
  4Q LOSS WILD-TYPE                                         1    96
D48V10, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   4                11
  BLACK OR AFRICAN AMERICAN                               9                 9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  34                96
[1] 5 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
  4Q LOSS MUTATED    2 38
  4Q LOSS WILD-TYPE  9 89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   38
  4Q LOSS WILD-TYPE    9   89
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              38                89
[1] 2 2
[1] FALSE
D48V12, continuous
D48V13, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   10  6
  4Q LOSS WILD-TYPE 38 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10    6
  4Q LOSS WILD-TYPE   38   13
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  TUMOR FREE              10                38
  WITH TUMOR               6                13
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  4Q LOSS MUTATED         1      4       1            39       3
  4Q LOSS WILD-TYPE       0      6       5           108       9
D48V14, multiclass
               clus
vv              4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      4                 6
  UKRAINE                     1                 5
  UNITED STATES              39               108
  VIETNAM                     3                 9
[1] 5 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                G1 G2 G3 G4 GX
  4Q LOSS MUTATED    0 17 31  0  0
  4Q LOSS WILD-TYPE 14 66 41  1  5
D48V15, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  G1               0                14
  G2              17                66
  G3              31                41
  G4               0                 1
  GX               0                 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"
D48V16, continuous
D48V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  4Q LOSS MUTATED                                             2
  4Q LOSS WILD-TYPE                                          19
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  4Q LOSS MUTATED                                        2
  4Q LOSS WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  4Q LOSS MUTATED                                                 0
  4Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  4Q LOSS MUTATED               12                  17
  4Q LOSS WILD-TYPE             24                  66
D48V18, multiclass
                                                 clus
vv                                                4Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                               12
  LIFELONG NON-SMOKER                                          17
                                                 clus
vv                                                4Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 24
  LIFELONG NON-SMOKER                                            66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  4Q LOSS MUTATED             4        8             4        4
  4Q LOSS WILD-TYPE          13       29             7        1
D48V20, multiclass
               clus
vv              4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COMBINATION                 4                13
  EXTERNAL                    8                29
  EXTERNAL BEAM               4                 7
  INTERNAL                    4                 1
[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"
D48V21, binary
                   cls
clus                0 1
  4Q LOSS MUTATED   5 1
  4Q LOSS WILD-TYPE 6 2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5    1
  4Q LOSS WILD-TYPE    6    2
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CGY               5                 6
  GY                1                 2
[1] 2 2
[1] FALSE
D48V22, continuous
D48V23, continuous
D48V24, continuous
D48V25, continuous
D48V26, continuous
D48V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  4Q LOSS MUTATED                                     0
  4Q LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  4Q LOSS MUTATED                                     3                       2
  4Q LOSS WILD-TYPE                                   3                       7
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  4Q LOSS MUTATED                         0                       1
  4Q LOSS WILD-TYPE                       1                       4
D48V28, multiclass
                                     clus
vv                                    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               3                 3
  OTHER LOCATION, SPECIFY                           2                 7
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 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)
  4Q LOSS MUTATED                                               0
  4Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  4Q LOSS MUTATED                                                2
  4Q LOSS WILD-TYPE                                              8
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  4Q LOSS MUTATED                                                                                  16
  4Q LOSS WILD-TYPE                                                                                38
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  4Q LOSS MUTATED                                                                                             18
  4Q LOSS WILD-TYPE                                                                                           59
D48V29, multiclass
                                                                                              clus
vv                                                                                             4Q 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)                         16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              18
                                                                                              clus
vv                                                                                             4Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               8
  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)                59
[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"
D48V30, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    9 19
  4Q LOSS WILD-TYPE 45 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9   19
  4Q LOSS WILD-TYPE   45   40
         clus
vv        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ABSENT                9                45
  PRESENT              19                40
[1] 2 2
[1] FALSE
D48V31, continuous
D48V32, continuous
D48V33, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   10 24
  4Q LOSS WILD-TYPE 25 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10   24
  4Q LOSS WILD-TYPE   25   57
                                          clus
vv                                         4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  10                25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              24                57
[1] 2 2
[1] FALSE
D48V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  4Q LOSS MUTATED       0                   30                   1
  4Q LOSS WILD-TYPE     3                   83                   4
D48V35, multiclass
                      clus
vv                     4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              30                83
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  4Q LOSS MUTATED              3           9         10
  4Q LOSS WILD-TYPE            5          31         30
D48V36, multiclass
              clus
vv             4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CURRENT USER               3                 5
  FORMER USER                9                31
  NEVER USED                10                30
[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, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   15  3
  4Q LOSS WILD-TYPE 58 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     15    3
  4Q LOSS WILD-TYPE   58   11
         clus
vv        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ABSENT               15                58
  PRESENT               3                11
[1] 2 2
[1] FALSE
D48V39, continuous
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                 8 
       TCGA-C5-A1MH        TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-EK-A2RO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  4Q LOSS MUTATED     0    0   6   12    4  2   1    2    0   4   1  0  1
  4Q LOSS WILD-TYPE   2    1  16   39   17  1   5    4    8   9   1  1  6
D48V40, multiclass
      clus
vv     4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                6                16
  T1B1              12                39
  T1B2               4                17
  T2                 2                 1
  T2A                1                 5
  T2A1               2                 4
  T2A2               0                 8
  T2B                4                 9
  T3B                1                 1
  T4                 0                 1
  TX                 1                 6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V41, continuous

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     4   7
  5P LOSS WILD-TYPE 133  25
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               158 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                25 
$`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        25.35 
TCGA-C5-A7UC TCGA-DS-A0VK TCGA-EA-A556 TCGA-EK-A2RM TCGA-LP-A4AW 
       17.19        36.76        14.89         2.24         0.89 

$`5P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        57.04        23.67        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ 
       31.40        46.32        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-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       83.05        78.35       100.14        38.43         0.82        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       182.93       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48         9.67        73.41        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
        9.34        13.61         2.73        87.75        58.88         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO 
       14.50         1.81        12.66        12.82         0.26         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91         0.69        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB 
       12.59        45.96         6.64         0.53         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN 
        4.04         0.03         0.36         1.18        23.70         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70         4.47         6.12         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        25.41        21.67        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX 
       20.48        15.58        10.06         5.13         0.10         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.89              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            68.84            182.93 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           25.350            12.935 
[1] "0.9 - 68.8 (25.4)"  "0.0 - 182.9 (12.9)"
[1] "hr=" "4"  
D49V2, continuous
                   vv
clus                T1 T2+T3+T4
  5P LOSS MUTATED    8        1
  5P LOSS WILD-TYPE 89       38
D49V3, multiclass
          clus
vv         5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                     8                89
  T2+T3+T4               1                38
[1] 2 2
[1] FALSE
D49V4, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    4  5
  5P LOSS WILD-TYPE 83 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    5
  5P LOSS WILD-TYPE   83   35
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               4                83
  1               5                35
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5P LOSS MUTATED    6  0  3
  5P LOSS WILD-TYPE 66  3 62
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               6                66
  M1               0                 3
  MX               3                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED               0                               10
  5P LOSS WILD-TYPE             2                              134
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5P LOSS MUTATED                                               0
  5P LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5P LOSS MUTATED                                     1
  5P LOSS WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5P LOSS MUTATED                                           1
  5P LOSS WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5P LOSS MUTATED                                              0
  5P LOSS WILD-TYPE                                            4
D49V6, multiclass
                                               clus
vv                                              5P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           10
  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                                              5P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            134
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D49V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5   7
  5P LOSS WILD-TYPE  22 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    7
  5P LOSS WILD-TYPE   22  142
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                5                22
  YES               7               142
[1] 2 2
[1] FALSE
D49V8, continuous
D49V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     1
  5P LOSS WILD-TYPE                                7    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED                           1
  5P LOSS WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           0    10
  5P LOSS WILD-TYPE                                         1   120
D49V10, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   1                14
  BLACK OR AFRICAN AMERICAN                               1                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               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"
D49V11, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  10
  5P LOSS WILD-TYPE  11 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   10
  5P LOSS WILD-TYPE   11  117
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              10               117
[1] 2 2
[1] FALSE
D49V12, continuous
D49V13, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  5
  5P LOSS WILD-TYPE 47 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    5
  5P LOSS WILD-TYPE   47   14
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  TUMOR FREE               1                47
  WITH TUMOR               5                14
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  5P LOSS MUTATED         0      1       0            10       1
  5P LOSS WILD-TYPE       1      9       6           137      11
D49V14, multiclass
               clus
vv              5P LOSS MUTATED 5P LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     0                 6
  UNITED STATES              10               137
  VIETNAM                     1                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"
                   vv
clus                G1 G2 G3 G4 GX
  5P LOSS MUTATED    1  3  8  0  0
  5P LOSS WILD-TYPE 13 80 64  1  5
D49V15, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  G1               1                13
  G2               3                80
  G3               8                64
  G4               0                 1
  GX               0                 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"
D49V16, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                24 
       TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL        TCGA-C5-A1BQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-C5-A1ME        TCGA-C5-A1MF        TCGA-C5-A2M2        TCGA-C5-A3HD 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-DS-A3LQ        TCGA-EX-A69M 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-HM-A3JK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D49V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5P LOSS MUTATED                                             1
  5P LOSS WILD-TYPE                                          20
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  5P LOSS MUTATED                                        2
  5P LOSS WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  5P LOSS MUTATED                                                 0
  5P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5P LOSS MUTATED                2                   4
  5P LOSS WILD-TYPE             34                  79
D49V18, multiclass
                                                 clus
vv                                                5P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                2
  LIFELONG NON-SMOKER                                           4
                                                 clus
vv                                                5P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 34
  LIFELONG NON-SMOKER                                            79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V19, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                46 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BJ        TCGA-C5-A1BL 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1BQ        TCGA-C5-A1M7        TCGA-C5-A1ME 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A2LS        TCGA-C5-A2LT        TCGA-C5-A2LV 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-C5-A2LZ        TCGA-C5-A2M2        TCGA-C5-A3HD 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-C5-A3HF        TCGA-C5-A7CJ        TCGA-C5-A7CL        TCGA-C5-A7CO 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-C5-A7UE        TCGA-C5-A7X8        TCGA-DR-A0ZM        TCGA-DS-A5RQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FU-A5XV        TCGA-FU-A770        TCGA-HM-A4S6        TCGA-HM-A6W2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH        TCGA-JW-A5VI 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-JW-A5VK        TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-RA-A741        TCGA-UC-A7PD 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  5P LOSS MUTATED             3        0             3        0
  5P LOSS WILD-TYPE          14       37             8        5
D49V20, multiclass
               clus
vv              5P LOSS MUTATED 5P LOSS WILD-TYPE
  COMBINATION                 3                14
  EXTERNAL                    0                37
  EXTERNAL BEAM               3                 8
  INTERNAL                    0                 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"
D49V21, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  0
  5P LOSS WILD-TYPE 10  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    0
  5P LOSS WILD-TYPE   10    3
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  CGY               1                10
  GY                0                 3
[1] 2 2
[1] FALSE
D49V22, continuous
D49V23, continuous
D49V24, continuous
D49V25, continuous
D49V26, continuous
D49V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  5P LOSS MUTATED                                     0
  5P LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  5P LOSS MUTATED                                     1                       1
  5P LOSS WILD-TYPE                                   5                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5P LOSS MUTATED                         0                       1
  5P LOSS WILD-TYPE                       1                       4
D49V28, multiclass
                                     clus
vv                                    5P LOSS MUTATED 5P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           1                 8
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 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)
  5P LOSS MUTATED                                               0
  5P LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5P LOSS MUTATED                                                2
  5P LOSS WILD-TYPE                                              8
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5P LOSS MUTATED                                                                                   3
  5P LOSS WILD-TYPE                                                                                51
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5P LOSS MUTATED                                                                                              4
  5P LOSS WILD-TYPE                                                                                           73
D49V29, multiclass
                                                                                              clus
vv                                                                                             5P 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)                          3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               4
                                                                                              clus
vv                                                                                             5P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               8
  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)                73
[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"
D49V30, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  6
  5P LOSS WILD-TYPE 53 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    6
  5P LOSS WILD-TYPE   53   53
         clus
vv        5P LOSS MUTATED 5P LOSS WILD-TYPE
  ABSENT                1                53
  PRESENT               6                53
[1] 2 2
[1] FALSE
D49V31, continuous
D49V32, continuous
D49V33, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    5  3
  5P LOSS WILD-TYPE 30 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    3
  5P LOSS WILD-TYPE   30   78
                                          clus
vv                                         5P LOSS MUTATED 5P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               3                78
[1] 2 2
[1] FALSE
D49V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  5P LOSS MUTATED       0                   10                   0
  5P LOSS WILD-TYPE     3                  103                   5
D49V35, multiclass
                      clus
vv                     5P LOSS MUTATED 5P LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              10               103
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5P LOSS MUTATED              0           1          2
  5P LOSS WILD-TYPE            8          39         38
D49V36, multiclass
              clus
vv             5P LOSS MUTATED 5P LOSS WILD-TYPE
  CURRENT USER               0                 8
  FORMER USER                1                39
  NEVER USED                 2                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"
D49V37, continuous
D49V38, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    5  1
  5P LOSS WILD-TYPE 68 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    1
  5P LOSS WILD-TYPE   68   13
         clus
vv        5P LOSS MUTATED 5P LOSS WILD-TYPE
  ABSENT                5                68
  PRESENT               1                13
[1] 2 2
[1] FALSE
D49V39, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                 8 
       TCGA-C5-A1BN        TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-EK-A2RO 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  5P LOSS MUTATED     1    0   3    4    0  0   0    0    0   0   1  0  0
  5P LOSS WILD-TYPE   1    1  19   47   21  3   6    6    8  13   1  1  7
D49V40, multiclass
      clus
vv     5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1A                1                 1
  T1A1               0                 1
  T1B                3                19
  T1B1               4                47
  T1B2               0                21
  T2                 0                 3
  T2A                0                 6
  T2A1               0                 6
  T2A2               0                 8
  T2B                0                13
  T3B                1                 1
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V41, continuous

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    22   9
  5Q LOSS WILD-TYPE 115  23
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               31               138 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                23 
$`5Q LOSS MUTATED`
TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BN TCGA-C5-A1M9 TCGA-C5-A1MH 
       11.44        68.84       144.16         5.46        35.01        38.99 
TCGA-C5-A1MI TCGA-C5-A3HE TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7UE TCGA-DR-A0ZL 
       35.61        18.02        25.35        17.19        85.55        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 
       36.76         2.66       117.99        12.36         1.32         1.35 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EK-A2IP TCGA-EK-A2RJ TCGA-EK-A2RM 
       14.50        14.89        14.96         6.64         1.18         2.24 
TCGA-EK-A3GK TCGA-FU-A23L TCGA-FU-A2QG TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-JW-A5VI 
        0.10        23.84         0.92        25.41        21.67        16.64 
TCGA-LP-A4AW 
        0.89 

$`5Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BK 
       49.48        57.04        23.67        18.74        36.56       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 
      173.29        82.85        19.86        67.46        31.40        46.32 
TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       30.21        57.73        53.16         0.46         2.43        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         0.82        52.01        17.85        20.42 
TCGA-C5-A7CG TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
      182.93       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM 
       60.69        94.95         9.34        13.61         2.73        58.88 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      118.65        22.98        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        0.76         1.74         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       14.50         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        1.48        13.91         0.69        14.99        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       12.59        45.96         0.53         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.03         0.36        23.70         0.10         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        6.12         1.22         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.97         1.12        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       26.56        36.36        14.43        19.33        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
       10.06         5.13         0.10         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        3.72         3.45         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.10              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           144.16            182.93 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            16.64             12.74 
[1] "0.1 - 144.2 (16.6)" "0.0 - 182.9 (12.7)"
[1] "hr=" "1.6"
D50V2, continuous
                   vv
clus                T1 T2+T3+T4
  5Q LOSS MUTATED   21        5
  5Q LOSS WILD-TYPE 76       34
D50V3, multiclass
          clus
vv         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                    21                76
  T2+T3+T4               5                34
[1] 2 2
[1] FALSE
D50V4, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   17  7
  5Q LOSS WILD-TYPE 70 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     17    7
  5Q LOSS WILD-TYPE   70   33
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              17                70
  1               7                33
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5Q LOSS MUTATED   16  0  9
  5Q LOSS WILD-TYPE 56  3 56
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              16                56
  M1               0                 3
  MX               9                56
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED               0                               30
  5Q LOSS WILD-TYPE             2                              114
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  5Q LOSS MUTATED                                               0
  5Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  5Q LOSS MUTATED                                     2
  5Q LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  5Q LOSS MUTATED                                           1
  5Q LOSS WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  5Q LOSS MUTATED                                              0
  5Q LOSS WILD-TYPE                                            4
D50V6, multiclass
                                               clus
vv                                              5Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              5Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            114
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     8  25
  5Q LOSS WILD-TYPE  19 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8   25
  5Q LOSS WILD-TYPE   19  124
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                8                19
  YES              25               124
[1] 2 2
[1] FALSE
D50V8, continuous
D50V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     4
  5Q LOSS WILD-TYPE                                6    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED                           2
  5Q LOSS WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           0    26
  5Q LOSS WILD-TYPE                                         1   104
D50V10, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   4                11
  BLACK OR AFRICAN AMERICAN                               2                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  26               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"
D50V11, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1  24
  5Q LOSS WILD-TYPE  10 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   24
  5Q LOSS WILD-TYPE   10  103
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              24               103
[1] 2 2
[1] FALSE
D50V12, continuous
D50V13, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    7  8
  5Q LOSS WILD-TYPE 41 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    8
  5Q LOSS WILD-TYPE   41   11
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  TUMOR FREE               7                41
  WITH TUMOR               8                11
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  5Q LOSS MUTATED         0      4       0            26       3
  5Q LOSS WILD-TYPE       1      6       6           121       9
D50V14, multiclass
               clus
vv              5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      4                 6
  UKRAINE                     0                 6
  UNITED STATES              26               121
  VIETNAM                     3                 9
[1] 5 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                G1 G2 G3 G4 GX
  5Q LOSS MUTATED    1 12 19  0  0
  5Q LOSS WILD-TYPE 13 71 53  1  5
D50V15, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  G1               1                13
  G2              12                71
  G3              19                53
  G4               0                 1
  GX               0                 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"
D50V16, continuous
D50V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  5Q LOSS MUTATED                                             3
  5Q LOSS WILD-TYPE                                          18
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  5Q LOSS MUTATED                                        2
  5Q LOSS WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  5Q LOSS MUTATED                                                 0
  5Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  5Q LOSS MUTATED                6                  14
  5Q LOSS WILD-TYPE             30                  69
D50V18, multiclass
                                                 clus
vv                                                5Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                6
  LIFELONG NON-SMOKER                                          14
                                                 clus
vv                                                5Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 30
  LIFELONG NON-SMOKER                                            69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  5Q LOSS MUTATED             5        4             4        0
  5Q LOSS WILD-TYPE          12       33             7        5
D50V20, multiclass
               clus
vv              5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COMBINATION                 5                12
  EXTERNAL                    4                33
  EXTERNAL BEAM               4                 7
  INTERNAL                    0                 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"
D50V21, binary
                   cls
clus                0 1
  5Q LOSS MUTATED   3 0
  5Q LOSS WILD-TYPE 8 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    0
  5Q LOSS WILD-TYPE    8    3
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CGY               3                 8
  GY                0                 3
[1] 2 2
[1] FALSE
D50V22, continuous
D50V23, continuous
D50V24, continuous
D50V25, continuous
D50V26, continuous
D50V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  5Q LOSS MUTATED                                     0
  5Q LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  5Q LOSS MUTATED                                     1                       3
  5Q LOSS WILD-TYPE                                   5                       6
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  5Q LOSS MUTATED                         0                       1
  5Q LOSS WILD-TYPE                       1                       4
D50V28, multiclass
                                     clus
vv                                    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           3                 6
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 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)
  5Q LOSS MUTATED                                               0
  5Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  5Q LOSS MUTATED                                                4
  5Q LOSS WILD-TYPE                                              6
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  5Q LOSS MUTATED                                                                                   9
  5Q LOSS WILD-TYPE                                                                                45
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  5Q LOSS MUTATED                                                                                             11
  5Q LOSS WILD-TYPE                                                                                           66
D50V29, multiclass
                                                                                              clus
vv                                                                                             5Q 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)                          9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              11
                                                                                              clus
vv                                                                                             5Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               6
  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)                66
[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"
D50V30, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    8 14
  5Q LOSS WILD-TYPE 46 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      8   14
  5Q LOSS WILD-TYPE   46   45
         clus
vv        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ABSENT                8                46
  PRESENT              14                45
[1] 2 2
[1] FALSE
D50V31, continuous
D50V32, continuous
D50V33, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    6 18
  5Q LOSS WILD-TYPE 29 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6   18
  5Q LOSS WILD-TYPE   29   63
                                          clus
vv                                         5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              18                63
[1] 2 2
[1] FALSE
D50V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  5Q LOSS MUTATED       0                   26                   0
  5Q LOSS WILD-TYPE     3                   87                   5
D50V35, multiclass
                      clus
vv                     5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              26                87
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  5Q LOSS MUTATED              1           7          7
  5Q LOSS WILD-TYPE            7          33         33
D50V36, multiclass
              clus
vv             5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                7                33
  NEVER USED                 7                33
[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
D50V38, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   13  4
  5Q LOSS WILD-TYPE 60 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     13    4
  5Q LOSS WILD-TYPE   60   10
         clus
vv        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ABSENT               13                60
  PRESENT               4                10
[1] 2 2
[1] FALSE
D50V39, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                 7 
       TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-EK-A2RO        TCGA-HM-A3JK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  5Q LOSS MUTATED     1    0   4   13    3  0   1    2    0   1   1  0  0
  5Q LOSS WILD-TYPE   1    1  18   38   18  3   5    4    8  12   1  1  7
D50V40, multiclass
      clus
vv     5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1A                1                 1
  T1A1               0                 1
  T1B                4                18
  T1B1              13                38
  T1B2               3                18
  T2                 0                 3
  T2A                1                 5
  T2A1               2                 4
  T2A2               0                 8
  T2B                1                12
  T3B                1                 1
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V41, continuous

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    20   3
  6P LOSS WILD-TYPE 117  29
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               23               146 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                3                29 
$`6P LOSS MUTATED`
TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A2LT TCGA-C5-A7CG TCGA-C5-A7CO TCGA-C5-A7UH 
       19.86        30.21        73.18       182.93        73.41        60.69 
TCGA-C5-A7X3 TCGA-DS-A0VK TCGA-EA-A3QE TCGA-EA-A44S TCGA-EA-A556 TCGA-EA-A6QX 
        9.34        36.76         1.18        12.66        14.89        13.58 
TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RC TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ 
       12.59         0.53         4.04         2.24         0.10         0.10 
TCGA-EX-A1H6 TCGA-FU-A3HY TCGA-IR-A3L7 TCGA-JW-A5VJ TCGA-Q1-A6DT 
        7.92         0.66       147.39        19.33         3.39 

$`6P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-A1MN TCGA-C5-A1MP 
       38.99        35.61         0.46         2.43        40.93         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-A7CH 
        0.82        52.01        18.02        17.85        20.42        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48         9.67        17.19        85.55 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL 
       94.95        13.61         2.73        87.75        58.88         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        8.28         0.76        12.36         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
        0.62        13.05        14.50         1.35         1.35        14.50 
TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
        1.81        12.82         0.26         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 
       14.99        14.96        13.48        45.96         6.64         0.59 
TCGA-EK-A2RB TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RO 
        0.07         0.03         0.36         1.18        23.70         0.07 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.03        20.35         6.94        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
        6.12         1.22        23.84         0.92         2.17         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
       14.93         4.11       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.10              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           182.93            177.04 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            12.66             13.74 
[1] "0.1 - 182.9 (12.7)" "0.0 - 177.0 (13.7)"
[1] "hr=" "1.6"
D51V2, continuous
                   vv
clus                T1 T2+T3+T4
  6P LOSS MUTATED   11        3
  6P LOSS WILD-TYPE 86       36
D51V3, multiclass
          clus
vv         6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                    11                86
  T2+T3+T4               3                36
[1] 2 2
[1] FALSE
D51V4, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    8  5
  6P LOSS WILD-TYPE 79 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      8    5
  6P LOSS WILD-TYPE   79   35
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               8                79
  1               5                35
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6P LOSS MUTATED    7  0  7
  6P LOSS WILD-TYPE 65  3 58
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               7                65
  M1               0                 3
  MX               7                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED               0                               22
  6P LOSS WILD-TYPE             2                              122
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6P LOSS MUTATED                                               0
  6P LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6P LOSS MUTATED                                     1
  6P LOSS WILD-TYPE                                  19
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6P LOSS MUTATED                                           1
  6P LOSS WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6P LOSS MUTATED                                              0
  6P LOSS WILD-TYPE                                            4
D51V6, multiclass
                                               clus
vv                                              6P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           22
  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                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            122
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2  22
  6P LOSS WILD-TYPE  25 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   22
  6P LOSS WILD-TYPE   25  127
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                2                25
  YES              22               127
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  1     1
  6P LOSS WILD-TYPE                                6    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED                           2
  6P LOSS WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           1    18
  6P LOSS WILD-TYPE                                         0   112
D51V10, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   1                14
  BLACK OR AFRICAN AMERICAN                               2                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  18               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"
D51V11, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  16
  6P LOSS WILD-TYPE  10 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   16
  6P LOSS WILD-TYPE   10  111
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              16               111
[1] 2 2
[1] FALSE
D51V12, continuous
D51V13, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    6  1
  6P LOSS WILD-TYPE 42 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      6    1
  6P LOSS WILD-TYPE   42   18
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  TUMOR FREE               6                42
  WITH TUMOR               1                18
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  6P LOSS MUTATED         0      2       1            20       1
  6P LOSS WILD-TYPE       1      8       5           127      11
D51V14, multiclass
               clus
vv              6P LOSS MUTATED 6P LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      2                 8
  UKRAINE                     1                 5
  UNITED STATES              20               127
  VIETNAM                     1                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"
                   vv
clus                G1 G2 G3 G4 GX
  6P LOSS MUTATED    1 11 11  0  1
  6P LOSS WILD-TYPE 13 72 61  1  4
D51V15, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  G1               1                13
  G2              11                72
  G3              11                61
  G4               0                 1
  GX               1                 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"
D51V16, continuous
D51V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6P LOSS MUTATED                                             3
  6P LOSS WILD-TYPE                                          18
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  6P LOSS MUTATED                                        1
  6P LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  6P LOSS MUTATED                                                 0
  6P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6P LOSS MUTATED                3                  10
  6P LOSS WILD-TYPE             33                  73
D51V18, multiclass
                                                 clus
vv                                                6P 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                                                3
  LIFELONG NON-SMOKER                                          10
                                                 clus
vv                                                6P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 33
  LIFELONG NON-SMOKER                                            73
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  6P LOSS MUTATED             0        4             3        2
  6P LOSS WILD-TYPE          17       33             8        3
D51V20, multiclass
               clus
vv              6P LOSS MUTATED 6P LOSS WILD-TYPE
  COMBINATION                 0                17
  EXTERNAL                    4                33
  EXTERNAL BEAM               3                 8
  INTERNAL                    2                 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"
D51V21, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    1  0
  6P LOSS WILD-TYPE 10  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    0
  6P LOSS WILD-TYPE   10    3
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  CGY               1                10
  GY                0                 3
[1] 2 2
[1] FALSE
D51V22, continuous
D51V23, continuous
D51V24, continuous
D51V25, continuous
D51V26, continuous
D51V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  6P LOSS MUTATED                                     0
  6P LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  6P LOSS MUTATED                                     0                       1
  6P LOSS WILD-TYPE                                   6                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6P LOSS MUTATED                         0                       1
  6P LOSS WILD-TYPE                       1                       4
D51V28, multiclass
[1] "Remove cluster labels:" "6P LOSS MUTATED"       
clus
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                21 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-DR-A0ZM        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A50E        TCGA-EK-A2RO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO        TCGA-HM-A4S6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK        TCGA-MU-A8JM 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-UC-A7PD 
"6P LOSS WILD-TYPE" 
                   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                                                1
  6P LOSS WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6P LOSS MUTATED                                                                                   7
  6P LOSS WILD-TYPE                                                                                47
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6P LOSS MUTATED                                                                                              8
  6P LOSS WILD-TYPE                                                                                           69
D51V29, multiclass
                                                                                              clus
vv                                                                                             6P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  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)               8
                                                                                              clus
vv                                                                                             6P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                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"
D51V30, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    5  8
  6P LOSS WILD-TYPE 49 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5    8
  6P LOSS WILD-TYPE   49   51
         clus
vv        6P LOSS MUTATED 6P LOSS WILD-TYPE
  ABSENT                5                49
  PRESENT               8                51
[1] 2 2
[1] FALSE
D51V31, continuous
D51V32, continuous
D51V33, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    6  8
  6P LOSS WILD-TYPE 29 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      6    8
  6P LOSS WILD-TYPE   29   73
                                          clus
vv                                         6P LOSS MUTATED 6P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               8                73
[1] 2 2
[1] FALSE
D51V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  6P LOSS MUTATED       0                   14                   0
  6P LOSS WILD-TYPE     3                   99                   5
D51V35, multiclass
                      clus
vv                     6P LOSS MUTATED 6P LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              14                99
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6P LOSS MUTATED              2           3          8
  6P LOSS WILD-TYPE            6          37         32
D51V36, multiclass
              clus
vv             6P LOSS MUTATED 6P LOSS WILD-TYPE
  CURRENT USER               2                 6
  FORMER USER                3                37
  NEVER USED                 8                32
[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, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   10  0
  6P LOSS WILD-TYPE 63 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     10    0
  6P LOSS WILD-TYPE   63   14
         clus
vv        6P LOSS MUTATED 6P LOSS WILD-TYPE
  ABSENT               10                63
  PRESENT               0                14
[1] 2 2
[1] FALSE
D51V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  6P LOSS MUTATED     0    0   4    6    1  0   0    0    1   2   0  0  1
  6P LOSS WILD-TYPE   2    1  18   45   20  3   6    6    7  11   2  1  6
D51V40, multiclass
      clus
vv     6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                4                18
  T1B1               6                45
  T1B2               1                20
  T2                 0                 3
  T2A                0                 6
  T2A1               0                 6
  T2A2               1                 7
  T2B                2                11
  T3B                0                 2
  T4                 0                 1
  TX                 1                 6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V41, continuous

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    36   3
  6Q LOSS WILD-TYPE 101  29
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               39               130 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                29 
$`6Q LOSS MUTATED`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A1BI TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1M8 
       49.48        23.67        36.56       173.29        82.85        30.21 
TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CO TCGA-C5-A7UH 
       73.18        73.45       182.93        25.35        73.41        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A44S TCGA-EA-A556 
       94.95         9.34        12.36         1.18        12.66        14.89 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RC 
       14.96        13.58        12.59         0.53         0.07         4.04 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H6 TCGA-FU-A23L TCGA-FU-A3HY 
        2.24         0.10         0.10         7.92        23.84         0.66 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-IR-A3L7 TCGA-JW-A5VJ TCGA-LP-A4AX 
        3.52         1.35         1.32       147.39        19.33         0.07 
TCGA-MU-A5YI TCGA-Q1-A5R2 TCGA-Q1-A6DT 
        0.03         3.45         3.39 

$`6Q LOSS WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BJ TCGA-C5-A1BK 
       57.04        11.44        68.84        18.74       144.16       177.04 
TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M9 
        5.46        19.86        67.46        31.40        46.32        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-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ 
       40.93         3.58        44.22        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         0.82        52.01        18.02        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48         9.67        17.19        85.55 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       13.61         2.73        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH 
      117.99       118.65        22.98        16.83        16.18         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28         0.76         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B 
       13.05        14.50         1.35         1.35        14.50         1.81 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
       12.82         0.26         1.48        13.91         0.69        14.99 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RD TCGA-EK-A2RE 
       13.48        45.96         6.64         0.59         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        1.18        23.70         0.07         0.10         0.03        20.35 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG 
        6.94        14.70         4.47         6.12         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17         1.02         1.45         1.58         1.48         0.82 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
        4.11       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VK 
       81.96        26.56        36.36        14.43        16.64        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 
       15.58        10.06         5.13         0.10         0.89         0.82 
TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
       13.87         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        3.72         5.85         3.72         5.75         4.80         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.03              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           182.93            177.04 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            12.66             13.74 
[1] "0.0 - 182.9 (12.7)" "0.0 - 177.0 (13.7)"
[1] "hr=" "3.3"
D52V2, continuous
                   vv
clus                T1 T2+T3+T4
  6Q LOSS MUTATED   21        7
  6Q LOSS WILD-TYPE 76       32
D52V3, multiclass
          clus
vv         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                    21                76
  T2+T3+T4               7                32
[1] 2 2
[1] FALSE
D52V4, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   15 10
  6Q LOSS WILD-TYPE 72 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15   10
  6Q LOSS WILD-TYPE   72   30
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              15                72
  1              10                30
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED   13  0 16
  6Q LOSS WILD-TYPE 59  3 49
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              13                59
  M1               0                 3
  MX              16                49
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED               0                               37
  6Q LOSS WILD-TYPE             2                              107
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  6Q LOSS MUTATED                                               0
  6Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  6Q LOSS MUTATED                                     4
  6Q LOSS WILD-TYPE                                  16
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  6Q LOSS MUTATED                                           1
  6Q LOSS WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  6Q LOSS MUTATED                                              0
  6Q LOSS WILD-TYPE                                            4
D52V6, multiclass
                                               clus
vv                                              6Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           37
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              6Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            107
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     5  37
  6Q LOSS WILD-TYPE  22 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5   37
  6Q LOSS WILD-TYPE   22  112
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                5                22
  YES              37               112
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  1     3
  6Q LOSS WILD-TYPE                                6    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED                           6
  6Q LOSS WILD-TYPE                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           1    30
  6Q LOSS WILD-TYPE                                         0   100
D52V10, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   3                12
  BLACK OR AFRICAN AMERICAN                               6                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  30               100
[1] 5 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
  6Q LOSS MUTATED    2 31
  6Q LOSS WILD-TYPE  9 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2   31
  6Q LOSS WILD-TYPE    9   96
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              31                96
[1] 2 2
[1] FALSE
D52V12, continuous
D52V13, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   11  2
  6Q LOSS WILD-TYPE 37 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     11    2
  6Q LOSS WILD-TYPE   37   17
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  TUMOR FREE              11                37
  WITH TUMOR               2                17
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  6Q LOSS MUTATED         0      3       1            35       3
  6Q LOSS WILD-TYPE       1      7       5           112       9
D52V14, multiclass
               clus
vv              6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      3                 7
  UKRAINE                     1                 5
  UNITED STATES              35               112
  VIETNAM                     3                 9
[1] 5 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                G1 G2 G3 G4 GX
  6Q LOSS MUTATED    2 19 20  0  1
  6Q LOSS WILD-TYPE 12 64 52  1  4
D52V15, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  G1               2                12
  G2              19                64
  G3              20                52
  G4               0                 1
  GX               1                 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"
D52V16, continuous
D52V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  6Q LOSS MUTATED                                             4
  6Q LOSS WILD-TYPE                                          17
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  6Q LOSS MUTATED                                        2
  6Q LOSS WILD-TYPE                                      6
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  6Q LOSS MUTATED                                                 0
  6Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  6Q LOSS MUTATED                8                  19
  6Q LOSS WILD-TYPE             28                  64
D52V18, multiclass
                                                 clus
vv                                                6Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                   4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                        2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED               0
  CURRENT SMOKER                                                8
  LIFELONG NON-SMOKER                                          19
                                                 clus
vv                                                6Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 28
  LIFELONG NON-SMOKER                                            64
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  6Q LOSS MUTATED             3        5             2        2
  6Q LOSS WILD-TYPE          14       32             9        3
D52V20, multiclass
               clus
vv              6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COMBINATION                 3                14
  EXTERNAL                    5                32
  EXTERNAL BEAM               2                 9
  INTERNAL                    2                 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"
D52V21, binary
                   cls
clus                0 1
  6Q LOSS MUTATED   2 0
  6Q LOSS WILD-TYPE 9 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      2    0
  6Q LOSS WILD-TYPE    9    3
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CGY               2                 9
  GY                0                 3
[1] 2 2
[1] FALSE
D52V22, continuous
D52V23, continuous
D52V24, continuous
D52V25, continuous
D52V26, continuous
D52V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  6Q LOSS MUTATED                                     0
  6Q LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  6Q LOSS MUTATED                                     1                       1
  6Q LOSS WILD-TYPE                                   5                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  6Q LOSS MUTATED                         0                       1
  6Q LOSS WILD-TYPE                       1                       4
D52V28, multiclass
                                     clus
vv                                    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           1                 8
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 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)
  6Q LOSS MUTATED                                               1
  6Q LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  6Q LOSS MUTATED                                                3
  6Q LOSS WILD-TYPE                                              7
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  6Q LOSS MUTATED                                                                                  13
  6Q LOSS WILD-TYPE                                                                                41
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  6Q LOSS MUTATED                                                                                             13
  6Q LOSS WILD-TYPE                                                                                           64
D52V29, multiclass
                                                                                              clus
vv                                                                                             6Q 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)                         13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              13
                                                                                              clus
vv                                                                                             6Q LOSS WILD-TYPE
  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)                           41
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                64
[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"
D52V30, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   11 13
  6Q LOSS WILD-TYPE 43 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     11   13
  6Q LOSS WILD-TYPE   43   46
         clus
vv        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ABSENT               11                43
  PRESENT              13                46
[1] 2 2
[1] FALSE
D52V31, continuous
D52V32, continuous
D52V33, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    5 20
  6Q LOSS WILD-TYPE 30 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5   20
  6Q LOSS WILD-TYPE   30   61
                                          clus
vv                                         6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              20                61
[1] 2 2
[1] FALSE
D52V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  6Q LOSS MUTATED       0                   26                   1
  6Q LOSS WILD-TYPE     3                   87                   4
D52V35, multiclass
                      clus
vv                     6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              26                87
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  6Q LOSS MUTATED              2           8         10
  6Q LOSS WILD-TYPE            6          32         30
D52V36, multiclass
              clus
vv             6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CURRENT USER               2                 6
  FORMER USER                8                32
  NEVER USED                10                30
[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
D52V38, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   16  4
  6Q LOSS WILD-TYPE 57 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     16    4
  6Q LOSS WILD-TYPE   57   10
         clus
vv        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ABSENT               16                57
  PRESENT               4                10
[1] 2 2
[1] FALSE
D52V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  6Q LOSS MUTATED     0    1   8   10    2  1   0    2    1   3   0  0  2
  6Q LOSS WILD-TYPE   2    0  14   41   19  2   6    4    7  10   2  1  5
D52V40, multiclass
      clus
vv     6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1A                0                 2
  T1A1               1                 0
  T1B                8                14
  T1B1              10                41
  T1B2               2                19
  T2                 1                 2
  T2A                0                 6
  T2A1               2                 4
  T2A2               1                 7
  T2B                3                10
  T3B                0                 2
  T4                 0                 1
  TX                 2                 5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V41, continuous

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    10   7
  7P LOSS WILD-TYPE 127  25
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               17               152 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                7                25 
$`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         7.33         0.76 
TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-RA-A741 
       14.50        14.96         2.24        20.35         3.88 

$`7P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        23.67        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-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A1MK 
       67.46        46.32        30.21        57.73         0.46         2.43 
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-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
      100.14        38.43         0.82        52.01        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93        25.35       101.82        15.48         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       73.41        17.19        85.55        60.69        94.95         9.34 
TCGA-C5-A7X8 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
        2.73        58.88        36.76         2.66       117.99       118.65 
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        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
       14.89         1.48        13.91         0.69        14.99        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
        0.10         0.07         0.10         0.10         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70         4.47         6.12         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        25.41        21.67        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH 
      147.39       137.16        66.81       117.40        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.76              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           134.33            182.93 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            20.35             12.74 
[1] "0.8 - 134.3 (20.4)" "0.0 - 182.9 (12.7)"
[1] "hr=" "1.9"
D53V2, continuous
                   vv
clus                T1 T2+T3+T4
  7P LOSS MUTATED    7        4
  7P LOSS WILD-TYPE 90       35
D53V3, multiclass
          clus
vv         7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1                     7                90
  T2+T3+T4               4                35
[1] 2 2
[1] FALSE
D53V4, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    5  5
  7P LOSS WILD-TYPE 82 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5    5
  7P LOSS WILD-TYPE   82   35
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               5                82
  1               5                35
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7P LOSS MUTATED    6  0  5
  7P LOSS WILD-TYPE 66  3 60
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               6                66
  M1               0                 3
  MX               5                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED               0                               15
  7P LOSS WILD-TYPE             2                              129
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7P LOSS MUTATED                                               0
  7P LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7P LOSS MUTATED                                     2
  7P LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7P LOSS MUTATED                                           0
  7P LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7P LOSS MUTATED                                              0
  7P LOSS WILD-TYPE                                            4
D53V6, multiclass
                                               clus
vv                                              7P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           15
  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                                              7P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            129
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D53V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     8   9
  7P LOSS WILD-TYPE  19 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8    9
  7P LOSS WILD-TYPE   19  140
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                8                19
  YES               9               140
[1] 2 2
[1] FALSE
D53V8, continuous
D53V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     3
  7P LOSS WILD-TYPE                                7    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED                           3
  7P LOSS WILD-TYPE                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           0    11
  7P LOSS WILD-TYPE                                         1   119
D53V10, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   3                12
  BLACK OR AFRICAN AMERICAN                               3                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               119
[1] 5 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
  7P LOSS MUTATED     0  15
  7P LOSS WILD-TYPE  11 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   15
  7P LOSS WILD-TYPE   11  112
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                11
  NOT HISPANIC OR LATINO              15               112
[1] 2 2
[1] FALSE
D53V12, continuous
D53V13, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    5  6
  7P LOSS WILD-TYPE 43 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5    6
  7P LOSS WILD-TYPE   43   13
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  TUMOR FREE               5                43
  WITH TUMOR               6                13
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  7P LOSS MUTATED         0      1       0            14       2
  7P LOSS WILD-TYPE       1      9       6           133      10
D53V14, multiclass
               clus
vv              7P LOSS MUTATED 7P LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     0                 6
  UNITED STATES              14               133
  VIETNAM                     2                10
[1] 5 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                G1 G2 G3 G4 GX
  7P LOSS MUTATED    0  7  9  0  1
  7P LOSS WILD-TYPE 14 76 63  1  4
D53V15, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  G1               0                14
  G2               7                76
  G3               9                63
  G4               0                 1
  GX               1                 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"
D53V16, continuous
D53V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7P LOSS MUTATED                                             2
  7P LOSS WILD-TYPE                                          19
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  7P LOSS MUTATED                                        1
  7P LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  7P LOSS MUTATED                                                 1
  7P LOSS WILD-TYPE                                               0
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7P LOSS MUTATED                3                   8
  7P LOSS WILD-TYPE             33                  75
D53V18, 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                                                3
  LIFELONG NON-SMOKER                                           8
                                                 clus
vv                                                7P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 0
  CURRENT SMOKER                                                 33
  LIFELONG NON-SMOKER                                            75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  7P LOSS MUTATED             5        3             2        1
  7P LOSS WILD-TYPE          12       34             9        4
D53V20, multiclass
               clus
vv              7P LOSS MUTATED 7P LOSS WILD-TYPE
  COMBINATION                 5                12
  EXTERNAL                    3                34
  EXTERNAL BEAM               2                 9
  INTERNAL                    1                 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"
D53V21, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    1  1
  7P LOSS WILD-TYPE 10  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    1
  7P LOSS WILD-TYPE   10    2
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  CGY               1                10
  GY                1                 2
[1] 2 2
[1] FALSE
D53V22, continuous
D53V23, continuous
D53V24, continuous
D53V25, continuous
D53V26, continuous
D53V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  7P LOSS MUTATED                                     0
  7P LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  7P LOSS MUTATED                                     2                       0
  7P LOSS WILD-TYPE                                   4                       9
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7P LOSS MUTATED                         0                       1
  7P LOSS WILD-TYPE                       1                       4
D53V28, multiclass
                                     clus
vv                                    7P LOSS MUTATED 7P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 4
  OTHER LOCATION, SPECIFY                           0                 9
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 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)
  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                                              8
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7P LOSS MUTATED                                                                                   6
  7P LOSS WILD-TYPE                                                                                48
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7P LOSS MUTATED                                                                                              6
  7P LOSS WILD-TYPE                                                                                           71
D53V29, 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)                          6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               6
                                                                                              clus
vv                                                                                             7P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               8
  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)                71
[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"
D53V30, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    4  7
  7P LOSS WILD-TYPE 50 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4    7
  7P LOSS WILD-TYPE   50   52
         clus
vv        7P LOSS MUTATED 7P LOSS WILD-TYPE
  ABSENT                4                50
  PRESENT               7                52
[1] 2 2
[1] FALSE
D53V31, continuous
D53V32, continuous
D53V33, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    6  7
  7P LOSS WILD-TYPE 29 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      6    7
  7P LOSS WILD-TYPE   29   74
                                          clus
vv                                         7P LOSS MUTATED 7P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   6                29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               7                74
[1] 2 2
[1] FALSE
D53V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  7P LOSS MUTATED       0                   12                   0
  7P LOSS WILD-TYPE     3                  101                   5
D53V35, multiclass
                      clus
vv                     7P LOSS MUTATED 7P LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              12               101
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7P LOSS MUTATED              0           6          3
  7P LOSS WILD-TYPE            8          34         37
D53V36, multiclass
              clus
vv             7P LOSS MUTATED 7P LOSS WILD-TYPE
  CURRENT USER               0                 8
  FORMER USER                6                34
  NEVER USED                 3                37
[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
D53V38, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    9  1
  7P LOSS WILD-TYPE 64 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      9    1
  7P LOSS WILD-TYPE   64   13
         clus
vv        7P LOSS MUTATED 7P LOSS WILD-TYPE
  ABSENT                9                64
  PRESENT               1                13
[1] 2 2
[1] FALSE
D53V39, continuous
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                 8 
       TCGA-C5-A1BN        TCGA-C5-A1MN        TCGA-C5-A1MP        TCGA-EK-A2RO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  7P LOSS MUTATED     0    0   1    5    1  1   0    1    0   1   1  0  0
  7P LOSS WILD-TYPE   2    1  21   46   20  2   6    5    8  12   1  1  7
D53V40, multiclass
      clus
vv     7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                1                21
  T1B1               5                46
  T1B2               1                20
  T2                 1                 2
  T2A                0                 6
  T2A1               1                 5
  T2A2               0                 8
  T2B                1                12
  T3B                1                 1
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V41, continuous

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    16  10
  7Q LOSS WILD-TYPE 121  22
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               26               143 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10                22 
$`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-A7CL TCGA-C5-A7X5 TCGA-DS-A7WH 
       40.93        73.45        83.05        15.48        13.61         7.33 
TCGA-EA-A1QS TCGA-EA-A439 TCGA-EA-A5ZF TCGA-EK-A2H0 TCGA-EK-A2RE TCGA-EK-A2RM 
        0.76        14.50        14.96        45.96         0.36         2.24 
TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-FU-A2QG TCGA-FU-A40J TCGA-HM-A3JJ TCGA-JW-A5VG 
        0.10        20.35         0.92         1.35        21.67        14.43 
TCGA-MY-A5BF TCGA-RA-A741 
        4.34         3.88 

$`7Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        23.67        68.84        18.74        36.56 
TCGA-C5-A1BJ TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85        19.86        67.46 
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-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 
        3.58        44.22        73.18        78.35       100.14        38.43 
TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
        0.82        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
       25.35       101.82       134.33         9.67        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL 
       85.55        60.69        94.95         9.34         2.73        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.83        16.18         8.28        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
        1.35         1.81        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EA-A78R 
        1.48        13.91         0.69        14.99        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       12.59         6.64         0.53         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.03         1.18        23.70         0.10         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.03         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22        23.84         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV 
        1.58         1.48         0.82         3.52         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.12        25.41        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       26.56        36.36        16.64        19.33        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       10.06         5.13         0.10         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA 
       13.87         0.03         5.42        29.72         0.07         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        3.72         3.45         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59        11.67        93.99 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.10              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            83.05            182.93 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           14.465            13.050 
[1] "0.1 - 83.0 (14.5)"  "0.0 - 182.9 (13.1)"
[1] "hr=" "3.4"
D54V2, continuous
                   vv
clus                T1 T2+T3+T4
  7Q LOSS MUTATED    9        8
  7Q LOSS WILD-TYPE 88       31
D54V3, multiclass
          clus
vv         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1                     9                88
  T2+T3+T4               8                31
[1] 2 2
[1] FALSE
D54V4, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    7  8
  7Q LOSS WILD-TYPE 80 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      7    8
  7Q LOSS WILD-TYPE   80   32
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               7                80
  1               8                32
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7Q LOSS MUTATED    5  0 11
  7Q LOSS WILD-TYPE 67  3 54
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               5                67
  M1               0                 3
  MX              11                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED               0                               22
  7Q LOSS WILD-TYPE             2                              122
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  7Q LOSS MUTATED                                               0
  7Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  7Q LOSS MUTATED                                     4
  7Q LOSS WILD-TYPE                                  16
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  7Q LOSS MUTATED                                           0
  7Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  7Q LOSS MUTATED                                              0
  7Q LOSS WILD-TYPE                                            4
D54V6, multiclass
                                               clus
vv                                              7Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           22
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              7Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            122
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D54V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    10  16
  7Q LOSS WILD-TYPE  17 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     10   16
  7Q LOSS WILD-TYPE   17  133
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               10                17
  YES              16               133
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  1     2
  7Q LOSS WILD-TYPE                                6    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED                           5
  7Q LOSS WILD-TYPE                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           0    18
  7Q LOSS WILD-TYPE                                         1   112
D54V10, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   2                13
  BLACK OR AFRICAN AMERICAN                               5                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  18               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"
D54V11, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  22
  7Q LOSS WILD-TYPE  10 105
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   22
  7Q LOSS WILD-TYPE   10  105
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              22               105
[1] 2 2
[1] FALSE
D54V12, continuous
D54V13, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    5  8
  7Q LOSS WILD-TYPE 43 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      5    8
  7Q LOSS WILD-TYPE   43   11
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  TUMOR FREE               5                43
  WITH TUMOR               8                11
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  7Q LOSS MUTATED         0      1       0            23       2
  7Q LOSS WILD-TYPE       1      9       6           124      10
D54V14, multiclass
               clus
vv              7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      1                 9
  UKRAINE                     0                 6
  UNITED STATES              23               124
  VIETNAM                     2                10
[1] 5 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                G1 G2 G3 G4 GX
  7Q LOSS MUTATED    1  9 15  0  1
  7Q LOSS WILD-TYPE 13 74 57  1  4
D54V15, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  G1               1                13
  G2               9                74
  G3              15                57
  G4               0                 1
  GX               1                 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"
D54V16, continuous
D54V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  7Q LOSS MUTATED                                             2
  7Q LOSS WILD-TYPE                                          19
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  7Q LOSS MUTATED                                        1
  7Q LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  7Q LOSS MUTATED                                                 0
  7Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  7Q LOSS MUTATED                7                  10
  7Q LOSS WILD-TYPE             29                  73
D54V18, 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                                                7
  LIFELONG NON-SMOKER                                          10
                                                 clus
vv                                                7Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 29
  LIFELONG NON-SMOKER                                            73
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  7Q LOSS MUTATED             6        3             3        2
  7Q LOSS WILD-TYPE          11       34             8        3
D54V20, multiclass
               clus
vv              7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COMBINATION                 6                11
  EXTERNAL                    3                34
  EXTERNAL BEAM               3                 8
  INTERNAL                    2                 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"
D54V21, binary
                   cls
clus                0 1
  7Q LOSS MUTATED   3 2
  7Q LOSS WILD-TYPE 8 1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    2
  7Q LOSS WILD-TYPE    8    1
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CGY               3                 8
  GY                2                 1
[1] 2 2
[1] FALSE
D54V22, continuous
D54V23, continuous
D54V24, continuous
D54V25, continuous
D54V26, continuous
D54V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  7Q LOSS MUTATED                                     0
  7Q LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  7Q LOSS MUTATED                                     2                       0
  7Q LOSS WILD-TYPE                                   4                       9
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  7Q LOSS MUTATED                         0                       1
  7Q LOSS WILD-TYPE                       1                       4
D54V28, multiclass
                                     clus
vv                                    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               2                 4
  OTHER LOCATION, SPECIFY                           0                 9
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 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)
  7Q LOSS MUTATED                                               0
  7Q LOSS WILD-TYPE                                             2
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  7Q LOSS MUTATED                                                3
  7Q LOSS WILD-TYPE                                              7
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  7Q LOSS MUTATED                                                                                   6
  7Q LOSS WILD-TYPE                                                                                48
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  7Q LOSS MUTATED                                                                                             13
  7Q LOSS WILD-TYPE                                                                                           64
D54V29, multiclass
                                                                                              clus
vv                                                                                             7Q 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)                          6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              13
                                                                                              clus
vv                                                                                             7Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               7
  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)                64
[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"
D54V30, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    4 13
  7Q LOSS WILD-TYPE 50 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4   13
  7Q LOSS WILD-TYPE   50   46
         clus
vv        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ABSENT                4                50
  PRESENT              13                46
[1] 2 2
[1] FALSE
D54V31, continuous
D54V32, continuous
D54V33, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    8 10
  7Q LOSS WILD-TYPE 27 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      8   10
  7Q LOSS WILD-TYPE   27   71
                                          clus
vv                                         7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   8                27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              10                71
[1] 2 2
[1] FALSE
D54V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  7Q LOSS MUTATED       1                   15                   0
  7Q LOSS WILD-TYPE     2                   98                   5
D54V35, multiclass
                      clus
vv                     7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  OTHER                              1                 2
  RADICAL HYSTERECTOMY              15                98
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  7Q LOSS MUTATED              1           8          5
  7Q LOSS WILD-TYPE            7          32         35
D54V36, multiclass
              clus
vv             7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                8                32
  NEVER USED                 5                35
[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
D54V38, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED   11  1
  7Q LOSS WILD-TYPE 62 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11    1
  7Q LOSS WILD-TYPE   62   13
         clus
vv        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ABSENT               11                62
  PRESENT               1                13
[1] 2 2
[1] FALSE
D54V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  7Q LOSS MUTATED     0    0   2    7    0  1   1    2    2   1   1  0  0
  7Q LOSS WILD-TYPE   2    1  20   44   21  2   5    4    6  12   1  1  7
D54V40, multiclass
      clus
vv     7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                2                20
  T1B1               7                44
  T1B2               0                21
  T2                 1                 2
  T2A                1                 5
  T2A1               2                 4
  T2A2               2                 6
  T2B                1                12
  T3B                1                 1
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V41, continuous

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    33  13
  8P LOSS WILD-TYPE 104  19
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               46               123 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13                19 
$`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-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A7UI 
        2.43        40.93        73.18        73.45        78.35        94.95 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DS-A0VK TCGA-DS-A0VN TCGA-DS-A7WI TCGA-EA-A1QT 
       13.61         2.73        36.76       118.65         8.28        12.36 
TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A556 TCGA-EK-A2GZ 
        1.32        14.50         1.81        12.66        14.89        12.59 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GN 
       45.96         0.53         2.24         0.07         0.10         0.03 
TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3WB TCGA-HM-A3JJ 
        6.94         6.12         1.22        23.84         0.82        21.67 
TCGA-IR-A3LA TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VL TCGA-JW-A852 TCGA-PN-A8MA 
      137.16        78.71        26.56        15.58         5.13         2.96 
TCGA-Q1-A6DT TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD 
        3.39        19.59         3.88        11.67 

$`8P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        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-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MP 
       67.46        53.16        38.99        35.61         0.46         3.58 
TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       44.22        83.05       100.14        38.43         0.82        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       182.93        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48         9.67        73.41        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7X3 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
       60.69         9.34        87.75        58.88         2.66       117.99 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-EA-A1QS TCGA-EA-A3HQ 
       22.98        16.83        16.18         7.33         0.76         1.74 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
        1.35        12.82         0.26         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2IP TCGA-EK-A2R7 
       14.99        14.96        13.58        13.48         6.64         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RN TCGA-EK-A3GK TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.10        20.35         7.92        14.70         4.47 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         3.52         1.35         1.32         1.97         1.12 
TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB 
       25.41        20.78        14.93         4.11       147.39        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
      117.40        96.95        81.96        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       19.33        20.48        10.06         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34         3.72         3.45         5.85         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-UC-A7PF 
        4.80         6.25        93.99 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           137.16            182.93 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           14.055            13.480 
[1] "0.0 - 137.2 (14.1)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.8"
D55V2, continuous
                   vv
clus                T1 T2+T3+T4
  8P LOSS MUTATED   23       12
  8P LOSS WILD-TYPE 74       27
D55V3, multiclass
          clus
vv         8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                    23                74
  T2+T3+T4              12                27
[1] 2 2
[1] FALSE
D55V4, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   24 10
  8P LOSS WILD-TYPE 63 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     24   10
  8P LOSS WILD-TYPE   63   30
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              24                63
  1              10                30
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED   21  0 14
  8P LOSS WILD-TYPE 51  3 51
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              21                51
  M1               0                 3
  MX              14                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED               0                               43
  8P LOSS WILD-TYPE             2                              101
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8P LOSS MUTATED                                               0
  8P LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8P LOSS MUTATED                                     3
  8P LOSS WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8P LOSS MUTATED                                           2
  8P LOSS WILD-TYPE                                         0
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8P LOSS MUTATED                                              1
  8P LOSS WILD-TYPE                                            3
D55V6, multiclass
                                               clus
vv                                              8P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           43
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              8P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            101
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    10  39
  8P LOSS WILD-TYPE  17 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     10   39
  8P LOSS WILD-TYPE   17  110
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               10                17
  YES              39               110
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  3     1
  8P LOSS WILD-TYPE                                4    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED                           8
  8P LOSS WILD-TYPE                        10
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           1    36
  8P LOSS WILD-TYPE                                         0    94
D55V10, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 4
  ASIAN                                                   1                14
  BLACK OR AFRICAN AMERICAN                               8                10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  36                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"
D55V11, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    4 32
  8P LOSS WILD-TYPE  7 95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4   32
  8P LOSS WILD-TYPE    7   95
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 7
  NOT HISPANIC OR LATINO              32                95
[1] 2 2
[1] FALSE
D55V12, continuous
D55V13, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   16  7
  8P LOSS WILD-TYPE 32 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     16    7
  8P LOSS WILD-TYPE   32   12
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  TUMOR FREE              16                32
  WITH TUMOR               7                12
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  8P LOSS MUTATED         1      3       2            42       1
  8P LOSS WILD-TYPE       0      7       4           105      11
D55V14, multiclass
               clus
vv              8P LOSS MUTATED 8P LOSS WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      3                 7
  UKRAINE                     2                 4
  UNITED STATES              42               105
  VIETNAM                     1                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"
                   vv
clus                G1 G2 G3 G4 GX
  8P LOSS MUTATED    3 18 25  1  2
  8P LOSS WILD-TYPE 11 65 47  0  3
D55V15, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  G1               3                11
  G2              18                65
  G3              25                47
  G4               1                 0
  GX               2                 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"
D55V16, continuous
D55V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8P LOSS MUTATED                                             6
  8P LOSS WILD-TYPE                                          15
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  8P LOSS MUTATED                                        1
  8P LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  8P LOSS MUTATED                                                 0
  8P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8P LOSS MUTATED                8                  22
  8P LOSS WILD-TYPE             28                  61
D55V18, multiclass
                                                 clus
vv                                                8P 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                                                8
  LIFELONG NON-SMOKER                                          22
                                                 clus
vv                                                8P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 28
  LIFELONG NON-SMOKER                                            61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  8P LOSS MUTATED             5       11             6        2
  8P LOSS WILD-TYPE          12       26             5        3
D55V20, multiclass
               clus
vv              8P LOSS MUTATED 8P LOSS WILD-TYPE
  COMBINATION                 5                12
  EXTERNAL                   11                26
  EXTERNAL BEAM               6                 5
  INTERNAL                    2                 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"
D55V21, binary
                   cls
clus                0 1
  8P LOSS MUTATED   4 2
  8P LOSS WILD-TYPE 7 1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    2
  8P LOSS WILD-TYPE    7    1
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  CGY               4                 7
  GY                2                 1
[1] 2 2
[1] FALSE
D55V22, continuous
D55V23, continuous
D55V24, continuous
D55V25, continuous
D55V26, continuous
D55V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  8P LOSS MUTATED                                     1
  8P LOSS WILD-TYPE                                   1
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  8P LOSS MUTATED                                     1                       3
  8P LOSS WILD-TYPE                                   5                       6
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8P LOSS MUTATED                         0                       2
  8P LOSS WILD-TYPE                       1                       3
D55V28, multiclass
                                     clus
vv                                    8P LOSS MUTATED 8P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               1                 1
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               1                 5
  OTHER LOCATION, SPECIFY                           3                 6
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           2                 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)
  8P LOSS MUTATED                                               1
  8P LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  8P LOSS MUTATED                                                1
  8P LOSS WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8P LOSS MUTATED                                                                                  15
  8P LOSS WILD-TYPE                                                                                39
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8P LOSS MUTATED                                                                                             24
  8P LOSS WILD-TYPE                                                                                           53
D55V29, multiclass
                                                                                              clus
vv                                                                                             8P LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                              1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                             1
  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 LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           39
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                53
[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"
D55V30, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   17 13
  8P LOSS WILD-TYPE 37 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     17   13
  8P LOSS WILD-TYPE   37   46
         clus
vv        8P LOSS MUTATED 8P LOSS WILD-TYPE
  ABSENT               17                37
  PRESENT              13                46
[1] 2 2
[1] FALSE
D55V31, continuous
D55V32, continuous
D55V33, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   10 24
  8P LOSS WILD-TYPE 25 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     10   24
  8P LOSS WILD-TYPE   25   57
                                          clus
vv                                         8P LOSS MUTATED 8P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  10                25
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              24                57
[1] 2 2
[1] FALSE
D55V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  8P LOSS MUTATED       0                   29                   1
  8P LOSS WILD-TYPE     3                   84                   4
D55V35, multiclass
                      clus
vv                     8P LOSS MUTATED 8P LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              29                84
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8P LOSS MUTATED              2          11         13
  8P LOSS WILD-TYPE            6          29         27
D55V36, multiclass
              clus
vv             8P LOSS MUTATED 8P LOSS WILD-TYPE
  CURRENT USER               2                 6
  FORMER USER               11                29
  NEVER USED                13                27
[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, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   22  3
  8P LOSS WILD-TYPE 51 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     22    3
  8P LOSS WILD-TYPE   51   11
         clus
vv        8P LOSS MUTATED 8P LOSS WILD-TYPE
  ABSENT               22                51
  PRESENT               3                11
[1] 2 2
[1] FALSE
D55V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  8P LOSS MUTATED     0    0   8   11    4  0   2    4    3   2   1  0  2
  8P LOSS WILD-TYPE   2    1  14   40   17  3   4    2    5  11   1  1  5
D55V40, multiclass
      clus
vv     8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                8                14
  T1B1              11                40
  T1B2               4                17
  T2                 0                 3
  T2A                2                 4
  T2A1               4                 2
  T2A2               3                 5
  T2B                2                11
  T3B                1                 1
  T4                 0                 1
  TX                 2                 5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V41, continuous

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    10   4
  8Q LOSS WILD-TYPE 127  28
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               155 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                28 
$`8Q LOSS MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A7X8 
       31.40        35.01        57.73        40.93        73.18         2.73 
TCGA-DS-A0VN TCGA-EA-A439 TCGA-EA-A43B TCGA-EK-A2RM TCGA-EX-A3L1 TCGA-PN-A8MA 
      118.65        14.50         1.81         2.24         6.94         2.96 
TCGA-R2-A69V TCGA-UC-A7PD 
       19.59        11.67 

$`8Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
       35.61         0.46         2.43         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         0.82        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       182.93        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      134.33        15.48         9.67        73.41        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       60.69        94.95         9.34        13.61        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
       36.76         2.66       117.99        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        7.33         8.28         0.76        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
        1.35        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91         0.69        14.99        14.96        13.58        13.48 
TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB 
       12.59        45.96         6.64         0.53         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN 
        4.04         0.03         0.36         1.18        23.70         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       14.70         4.47         6.12         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        0.82         3.52         1.35         1.32         1.97         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36        14.43        16.64        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       15.58        10.06         5.13         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV 
        4.34         3.72         3.45         5.85         3.39         3.72 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PF 
        5.75         4.80         6.25         3.88        93.99 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.81              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           118.65            182.93 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           17.045            13.480 
[1] "1.8 - 118.7 (17.0)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.4"
D56V2, continuous
                   vv
clus                T1 T2+T3+T4
  8Q LOSS MUTATED    6        5
  8Q LOSS WILD-TYPE 91       34
D56V3, multiclass
          clus
vv         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1                     6                91
  T2+T3+T4               5                34
[1] 2 2
[1] FALSE
D56V4, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    9  2
  8Q LOSS WILD-TYPE 78 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9    2
  8Q LOSS WILD-TYPE   78   38
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               9                78
  1               2                38
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8Q LOSS MUTATED   11  0  0
  8Q LOSS WILD-TYPE 61  3 65
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0              11                61
  M1               0                 3
  MX               0                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED               0                               11
  8Q LOSS WILD-TYPE             2                              133
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  8Q LOSS MUTATED                                               0
  8Q LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  8Q LOSS MUTATED                                     3
  8Q LOSS WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  8Q LOSS MUTATED                                           0
  8Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  8Q LOSS MUTATED                                              1
  8Q LOSS WILD-TYPE                                            3
D56V6, multiclass
                                               clus
vv                                              8Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           11
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              8Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            133
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     5  10
  8Q LOSS WILD-TYPE  22 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5   10
  8Q LOSS WILD-TYPE   22  139
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                5                22
  YES              10               139
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  1     1
  8Q LOSS WILD-TYPE                                6    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED                           1
  8Q LOSS WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           0    12
  8Q LOSS WILD-TYPE                                         1   118
D56V10, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   1                14
  BLACK OR AFRICAN AMERICAN                               1                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               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"
D56V11, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  12
  8Q LOSS WILD-TYPE  10 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   12
  8Q LOSS WILD-TYPE   10  115
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              12               115
[1] 2 2
[1] FALSE
D56V12, continuous
D56V13, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    5  2
  8Q LOSS WILD-TYPE 43 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    2
  8Q LOSS WILD-TYPE   43   17
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  TUMOR FREE               5                43
  WITH TUMOR               2                17
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  8Q LOSS MUTATED         1      0       1            12       1
  8Q LOSS WILD-TYPE       0     10       5           135      11
D56V14, multiclass
               clus
vv              8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      0                10
  UKRAINE                     1                 5
  UNITED STATES              12               135
  VIETNAM                     1                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"
                   vv
clus                G1 G2 G3 G4 GX
  8Q LOSS MUTATED    1  6  8  0  0
  8Q LOSS WILD-TYPE 13 77 64  1  5
D56V15, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  G1               1                13
  G2               6                77
  G3               8                64
  G4               0                 1
  GX               0                 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"
D56V16, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                24 
       TCGA-BI-A0VR        TCGA-C5-A1BJ        TCGA-C5-A1BL        TCGA-C5-A1BQ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C5-A1MF        TCGA-C5-A1MH        TCGA-C5-A2M2        TCGA-C5-A3HD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C5-A7CM        TCGA-C5-A7CO        TCGA-DS-A3LQ        TCGA-EX-A69M 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3TX        TCGA-FU-A3WB        TCGA-HM-A3JK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3L7        TCGA-IR-A3LB        TCGA-IR-A3LH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MU-A5YI        TCGA-MU-A8JM        TCGA-Q1-A6DW        TCGA-RA-A741 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D56V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  8Q LOSS MUTATED                                             1
  8Q LOSS WILD-TYPE                                          20
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  8Q LOSS MUTATED                                        0
  8Q LOSS WILD-TYPE                                      8
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  8Q LOSS MUTATED                                                 0
  8Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  8Q LOSS MUTATED                4                   8
  8Q LOSS WILD-TYPE             32                  75
D56V18, multiclass
                                                 clus
vv                                                8Q 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                                           8
                                                 clus
vv                                                8Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 32
  LIFELONG NON-SMOKER                                            75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  8Q LOSS MUTATED             2        4             3        1
  8Q LOSS WILD-TYPE          15       33             8        4
D56V20, multiclass
               clus
vv              8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COMBINATION                 2                15
  EXTERNAL                    4                33
  EXTERNAL BEAM               3                 8
  INTERNAL                    1                 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"
D56V21, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  1
  8Q LOSS WILD-TYPE 10  2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    1
  8Q LOSS WILD-TYPE   10    2
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CGY               1                10
  GY                1                 2
[1] 2 2
[1] FALSE
D56V22, continuous
D56V23, continuous
D56V24, continuous
D56V25, continuous
D56V26, continuous
D56V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  8Q LOSS MUTATED                                     0
  8Q LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  8Q LOSS MUTATED                                     0                       2
  8Q LOSS WILD-TYPE                                   6                       7
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  8Q LOSS MUTATED                         0                       0
  8Q LOSS WILD-TYPE                       1                       5
D56V28, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                21 
       TCGA-BI-A20A        TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-C5-A2LX        TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DS-A0VM        TCGA-DS-A3LQ        TCGA-EA-A50E        TCGA-EK-A2RN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MU-A8JM 
"8Q LOSS WILD-TYPE" 
                   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                                                1
  8Q LOSS WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  8Q LOSS MUTATED                                                                                   2
  8Q LOSS WILD-TYPE                                                                                52
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  8Q LOSS MUTATED                                                                                             10
  8Q LOSS WILD-TYPE                                                                                           67
D56V29, multiclass
                                                                                              clus
vv                                                                                             8Q 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)                          2
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              10
                                                                                              clus
vv                                                                                             8Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  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)                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"
D56V30, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    5  6
  8Q LOSS WILD-TYPE 49 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    6
  8Q LOSS WILD-TYPE   49   53
         clus
vv        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ABSENT                5                49
  PRESENT               6                53
[1] 2 2
[1] FALSE
D56V31, continuous
D56V32, continuous
D56V33, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    5  4
  8Q LOSS WILD-TYPE 30 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5    4
  8Q LOSS WILD-TYPE   30   77
                                          clus
vv                                         8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   5                30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               4                77
[1] 2 2
[1] FALSE
D56V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  8Q LOSS MUTATED       0                   10                   0
  8Q LOSS WILD-TYPE     3                  103                   5
D56V35, multiclass
                      clus
vv                     8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              10               103
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  8Q LOSS MUTATED              2           7          1
  8Q LOSS WILD-TYPE            6          33         39
D56V36, multiclass
              clus
vv             8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CURRENT USER               2                 6
  FORMER USER                7                33
  NEVER USED                 1                39
[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, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    7  1
  8Q LOSS WILD-TYPE 66 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7    1
  8Q LOSS WILD-TYPE   66   13
         clus
vv        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ABSENT                7                66
  PRESENT               1                13
[1] 2 2
[1] FALSE
D56V39, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                 8 
       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-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  8Q LOSS MUTATED     0    0   3    2    1  0   1    2    0   1   1  0  0
  8Q LOSS WILD-TYPE   2    1  19   49   20  3   5    4    8  12   1  1  7
D56V40, multiclass
      clus
vv     8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1A                0                 2
  T1A1               0                 1
  T1B                3                19
  T1B1               2                49
  T1B2               1                20
  T2                 0                 3
  T2A                1                 5
  T2A1               2                 4
  T2A2               0                 8
  T2B                1                12
  T3B                1                 1
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V41, continuous

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    22   9
  9P LOSS WILD-TYPE 115  23
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               31               138 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                9                23 
$`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        25.35        60.69         9.34        13.61 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S 
        0.76        12.36         1.32         1.35         1.81        12.66 
TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EX-A69M TCGA-FU-A3YQ 
       12.59         0.53         0.36         2.24         6.12         3.52 
TCGA-HM-A3JJ TCGA-LP-A4AW TCGA-MU-A5YI TCGA-MY-A5BD TCGA-Q1-A5R1 TCGA-Q1-A5R2 
       21.67         0.89         0.03        29.72         3.72         3.45 
TCGA-Q1-A6DT 
        3.39 

$`9P LOSS 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-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
      177.04       173.29        82.85         5.46        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP 
       46.32        30.21        53.16        38.99         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         0.82        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 
      182.93       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       17.19        85.55        94.95         2.73        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76         2.66       117.99       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT 
       16.18         7.33         8.28         1.74         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A4BA 
       13.05         1.18        14.50         1.35        14.50        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        0.26        14.89         1.48        13.91         0.69        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 
       14.96        13.58        13.48        45.96         6.64         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN 
        0.07         4.04         0.03         1.18        23.70         0.10 
TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.07         0.10         0.10         0.03        20.35         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        6.94        14.70         4.47         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        2.17         0.66         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA 
        0.82         1.35         1.32         1.97         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         4.11       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       14.43        16.64        19.33        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM 
        5.13         0.10         0.07         0.82        13.87         5.42 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        0.07         4.34         2.96         5.85         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.03              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           144.16            182.93 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            9.340            14.465 
[1] "0.0 - 144.2 (9.3)"  "0.0 - 182.9 (14.5)"
[1] "hr=" "2.6"
D57V2, continuous
                   vv
clus                T1 T2+T3+T4
  9P LOSS MUTATED   15        5
  9P LOSS WILD-TYPE 82       34
D57V3, multiclass
          clus
vv         9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                    15                82
  T2+T3+T4               5                34
[1] 2 2
[1] FALSE
D57V4, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   15  4
  9P LOSS WILD-TYPE 72 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     15    4
  9P LOSS WILD-TYPE   72   36
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              15                72
  1               4                36
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED   14  0  8
  9P LOSS WILD-TYPE 58  3 57
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              14                58
  M1               0                 3
  MX               8                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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED               0                               30
  9P LOSS WILD-TYPE             2                              114
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9P LOSS MUTATED                                               0
  9P LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9P LOSS MUTATED                                     3
  9P LOSS WILD-TYPE                                  17
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9P LOSS MUTATED                                           0
  9P LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9P LOSS MUTATED                                              1
  9P LOSS WILD-TYPE                                            3
D57V6, multiclass
                                               clus
vv                                              9P LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                1
                                               clus
vv                                              9P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            114
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  3
[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"
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     6  28
  9P LOSS WILD-TYPE  21 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6   28
  9P LOSS WILD-TYPE   21  121
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                6                21
  YES              28               121
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     2
  9P LOSS WILD-TYPE                                7    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED                           5
  9P LOSS WILD-TYPE                        13
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           0    27
  9P LOSS WILD-TYPE                                         1   103
D57V10, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   2                13
  BLACK OR AFRICAN AMERICAN                               5                13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  27               103
[1] 5 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
  9P LOSS MUTATED     1  26
  9P LOSS WILD-TYPE  10 101
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   26
  9P LOSS WILD-TYPE   10  101
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                10
  NOT HISPANIC OR LATINO              26               101
[1] 2 2
[1] FALSE
D57V12, continuous
D57V13, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    7  4
  9P LOSS WILD-TYPE 41 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7    4
  9P LOSS WILD-TYPE   41   15
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  TUMOR FREE               7                41
  WITH TUMOR               4                15
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  9P LOSS MUTATED         0      4       2            26       2
  9P LOSS WILD-TYPE       1      6       4           121      10
D57V14, multiclass
               clus
vv              9P LOSS MUTATED 9P LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      4                 6
  UKRAINE                     2                 4
  UNITED STATES              26               121
  VIETNAM                     2                10
[1] 5 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                G1 G2 G3 G4 GX
  9P LOSS MUTATED    4 17 11  0  1
  9P LOSS WILD-TYPE 10 66 61  1  4
D57V15, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  G1               4                10
  G2              17                66
  G3              11                61
  G4               0                 1
  GX               1                 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"
D57V16, continuous
D57V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9P LOSS MUTATED                                             3
  9P LOSS WILD-TYPE                                          18
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  9P LOSS MUTATED                                        1
  9P LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  9P LOSS MUTATED                                                 0
  9P LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9P LOSS MUTATED                3                  18
  9P LOSS WILD-TYPE             33                  65
D57V18, multiclass
                                                 clus
vv                                                9P 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                                                3
  LIFELONG NON-SMOKER                                          18
                                                 clus
vv                                                9P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 33
  LIFELONG NON-SMOKER                                            65
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  9P LOSS MUTATED             4        4             2        1
  9P LOSS WILD-TYPE          13       33             9        4
D57V20, multiclass
               clus
vv              9P LOSS MUTATED 9P LOSS WILD-TYPE
  COMBINATION                 4                13
  EXTERNAL                    4                33
  EXTERNAL BEAM               2                 9
  INTERNAL                    1                 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"
D57V21, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    1  0
  9P LOSS WILD-TYPE 10  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1    0
  9P LOSS WILD-TYPE   10    3
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  CGY               1                10
  GY                0                 3
[1] 2 2
[1] FALSE
D57V22, continuous
D57V23, continuous
D57V24, continuous
D57V25, continuous
D57V26, continuous
D57V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  9P LOSS MUTATED                                     0
  9P LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  9P LOSS MUTATED                                     1                       0
  9P LOSS WILD-TYPE                                   5                       9
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9P LOSS MUTATED                         0                       0
  9P LOSS WILD-TYPE                       1                       5
D57V28, multiclass
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                22 
       TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM        TCGA-C5-A2LX 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A50E        TCGA-EK-A2RN 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-UC-A7PD 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
                   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                                                2
  9P LOSS WILD-TYPE                                              8
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9P LOSS MUTATED                                                                                  14
  9P LOSS WILD-TYPE                                                                                40
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9P LOSS MUTATED                                                                                             10
  9P LOSS WILD-TYPE                                                                                           67
D57V29, multiclass
                                                                                              clus
vv                                                                                             9P 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)              10
                                                                                              clus
vv                                                                                             9P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               8
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           40
  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"
D57V30, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    7  9
  9P LOSS WILD-TYPE 47 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7    9
  9P LOSS WILD-TYPE   47   50
         clus
vv        9P LOSS MUTATED 9P LOSS WILD-TYPE
  ABSENT                7                47
  PRESENT               9                50
[1] 2 2
[1] FALSE
D57V31, continuous
D57V32, continuous
D57V33, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    7 16
  9P LOSS WILD-TYPE 28 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7   16
  9P LOSS WILD-TYPE   28   65
                                          clus
vv                                         9P LOSS MUTATED 9P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   7                28
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              16                65
[1] 2 2
[1] FALSE
D57V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  9P LOSS MUTATED       0                   18                   0
  9P LOSS WILD-TYPE     3                   95                   5
D57V35, multiclass
                      clus
vv                     9P LOSS MUTATED 9P LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              18                95
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9P LOSS MUTATED              1           9          7
  9P LOSS WILD-TYPE            7          31         33
D57V36, multiclass
              clus
vv             9P LOSS MUTATED 9P LOSS WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                9                31
  NEVER USED                 7                33
[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
D57V38, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   11  2
  9P LOSS WILD-TYPE 62 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     11    2
  9P LOSS WILD-TYPE   62   12
         clus
vv        9P LOSS MUTATED 9P LOSS WILD-TYPE
  ABSENT               11                62
  PRESENT               2                12
[1] 2 2
[1] FALSE
D57V39, continuous
[1] "Remove cluster labels:" "9P LOSS MUTATED"       
clus
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                 8 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1MP        TCGA-EK-A2RO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  9P LOSS MUTATED     1    1   2   10    1  0   1    0    2   1   1  0  2
  9P LOSS WILD-TYPE   1    0  20   41   20  3   5    6    6  12   1  1  5
D57V40, multiclass
      clus
vv     9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1A                1                 1
  T1A1               1                 0
  T1B                2                20
  T1B1              10                41
  T1B2               1                20
  T2                 0                 3
  T2A                1                 5
  T2A1               0                 6
  T2A2               2                 6
  T2B                1                12
  T3B                1                 1
  T4                 0                 1
  TX                 2                 5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V41, continuous

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    19   8
  9Q LOSS WILD-TYPE 118  24
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               27               142 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8                24 
$`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-EA-A1QS 
       25.35        60.69         9.34        13.61         2.73         0.76 
TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A43B TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RE 
       12.36         1.35         1.81        12.59         0.53         0.36 
TCGA-EK-A2RM TCGA-EX-A69M TCGA-HM-A3JJ TCGA-IR-A3LF TCGA-MU-A5YI TCGA-MY-A5BD 
        2.24         6.12        21.67        96.95         0.03        29.72 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        2.96         3.72         3.45 

$`9Q LOSS 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-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-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MK 
       67.46        46.32        30.21        53.16        38.99         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-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43         0.82        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       182.93       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-DR-A0ZL 
        9.67        73.41        17.19        85.55        94.95        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.83        16.18         7.33         8.28         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       14.50        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91         0.69        14.99        14.96        13.58        13.48 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       45.96         6.64         0.59         0.07         4.04         0.03 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        1.18        23.70         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70         4.47 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17         0.66         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 
        1.32         1.97         1.12        25.41        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LH 
        4.11       147.39       137.16        66.81       117.40        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BE TCGA-MY-A5BF 
        0.07         0.82        13.87         5.42         0.07         4.34 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        5.85         3.39         3.72         5.75         4.80         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.03              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            96.95            182.93 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             9.34             14.17 
[1] "0.0 - 97.0 (9.3)"   "0.0 - 182.9 (14.2)"
[1] "hr=" "2.9"
D58V2, continuous
                   vv
clus                T1 T2+T3+T4
  9Q LOSS MUTATED   13        5
  9Q LOSS WILD-TYPE 84       34
D58V3, multiclass
          clus
vv         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                    13                84
  T2+T3+T4               5                34
[1] 2 2
[1] FALSE
D58V4, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   13  4
  9Q LOSS WILD-TYPE 74 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     13    4
  9Q LOSS WILD-TYPE   74   36
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              13                74
  1               4                36
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED   13  0  6
  9Q LOSS WILD-TYPE 59  3 59
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              13                59
  M1               0                 3
  MX               6                59
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED               0                               22
  9Q LOSS WILD-TYPE             2                              122
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  9Q LOSS MUTATED                                               1
  9Q LOSS WILD-TYPE                                             3
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  9Q LOSS MUTATED                                     4
  9Q LOSS WILD-TYPE                                  16
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  9Q LOSS MUTATED                                           0
  9Q LOSS WILD-TYPE                                         2
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  9Q LOSS MUTATED                                              2
  9Q LOSS WILD-TYPE                                            2
D58V6, multiclass
                                               clus
vv                                              9Q LOSS MUTATED
  ADENOSQUAMOUS                                               0
  CERVICAL SQUAMOUS CELL CARCINOMA                           22
  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                                              9Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 2
  CERVICAL SQUAMOUS CELL CARCINOMA                            122
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  2
[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"
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     4  25
  9Q LOSS WILD-TYPE  23 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4   25
  9Q LOSS WILD-TYPE   23  124
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                4                23
  YES              25               124
[1] 2 2
[1] FALSE
D58V8, continuous
D58V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     0
  9Q LOSS WILD-TYPE                                7    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED                           6
  9Q LOSS WILD-TYPE                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           0    23
  9Q LOSS WILD-TYPE                                         1   107
D58V10, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 7
  ASIAN                                                   0                15
  BLACK OR AFRICAN AMERICAN                               6                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  23               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"
D58V11, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2  21
  9Q LOSS WILD-TYPE   9 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   21
  9Q LOSS WILD-TYPE    9  106
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              21               106
[1] 2 2
[1] FALSE
D58V12, continuous
D58V13, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    5  4
  9Q LOSS WILD-TYPE 43 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5    4
  9Q LOSS WILD-TYPE   43   15
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  TUMOR FREE               5                43
  WITH TUMOR               4                15
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  9Q LOSS MUTATED         1      3       1            24       0
  9Q LOSS WILD-TYPE       0      7       5           123      12
D58V14, multiclass
               clus
vv              9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NIGERIA                     1                 0
  RUSSIA                      3                 7
  UKRAINE                     1                 5
  UNITED STATES              24               123
  VIETNAM                     0                12
[1] 5 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                G1 G2 G3 G4 GX
  9Q LOSS MUTATED    2 15 11  0  0
  9Q LOSS WILD-TYPE 12 68 61  1  5
D58V15, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  G1               2                12
  G2              15                68
  G3              11                61
  G4               0                 1
  GX               0                 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"
D58V16, continuous
D58V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  9Q LOSS MUTATED                                             2
  9Q LOSS WILD-TYPE                                          19
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  9Q LOSS MUTATED                                        1
  9Q LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  9Q LOSS MUTATED                                                 0
  9Q LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  9Q LOSS MUTATED                2                  15
  9Q LOSS WILD-TYPE             34                  68
D58V18, multiclass
                                                 clus
vv                                                9Q 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                                          15
                                                 clus
vv                                                9Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 34
  LIFELONG NON-SMOKER                                            68
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  9Q LOSS MUTATED             2        6             2        1
  9Q LOSS WILD-TYPE          15       31             9        4
D58V20, multiclass
               clus
vv              9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COMBINATION                 2                15
  EXTERNAL                    6                31
  EXTERNAL BEAM               2                 9
  INTERNAL                    1                 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"
D58V21, binary
                   cls
clus                0 1
  9Q LOSS MUTATED   2 0
  9Q LOSS WILD-TYPE 9 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2    0
  9Q LOSS WILD-TYPE    9    3
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CGY               2                 9
  GY                0                 3
[1] 2 2
[1] FALSE
D58V22, continuous
D58V23, continuous
D58V24, continuous
D58V25, continuous
D58V26, continuous
D58V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  9Q LOSS MUTATED                                     0
  9Q LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  9Q LOSS MUTATED                                     1                       0
  9Q LOSS WILD-TYPE                                   5                       9
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  9Q LOSS MUTATED                         0                       0
  9Q LOSS WILD-TYPE                       1                       5
D58V28, multiclass
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                22 
       TCGA-C5-A0TN        TCGA-C5-A1BE        TCGA-C5-A1BM        TCGA-C5-A2LX 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A50E        TCGA-EK-A2RN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EK-A2RO        TCGA-EX-A1H5        TCGA-EX-A449        TCGA-FU-A3EO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-HM-A4S6        TCGA-IR-A3LH        TCGA-IR-A3LI        TCGA-IR-A3LK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-MU-A8JM        TCGA-UC-A7PD 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
                   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                                                1
  9Q LOSS WILD-TYPE                                              9
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  9Q LOSS MUTATED                                                                                  13
  9Q LOSS WILD-TYPE                                                                                41
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  9Q LOSS MUTATED                                                                                              7
  9Q LOSS WILD-TYPE                                                                                           70
D58V29, multiclass
                                                                                              clus
vv                                                                                             9Q 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)                         13
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               7
                                                                                              clus
vv                                                                                             9Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                           41
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                70
[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"
D58V30, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    7 10
  9Q LOSS WILD-TYPE 47 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      7   10
  9Q LOSS WILD-TYPE   47   49
         clus
vv        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ABSENT                7                47
  PRESENT              10                49
[1] 2 2
[1] FALSE
D58V31, continuous
D58V32, continuous
D58V33, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    4 13
  9Q LOSS WILD-TYPE 31 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4   13
  9Q LOSS WILD-TYPE   31   68
                                          clus
vv                                         9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   4                31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              13                68
[1] 2 2
[1] FALSE
D58V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  9Q LOSS MUTATED       0                   14                   1
  9Q LOSS WILD-TYPE     3                   99                   4
D58V35, multiclass
                      clus
vv                     9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  OTHER                              0                 3
  RADICAL HYSTERECTOMY              14                99
  SIMPLE HYSTERECTOMY                1                 4
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  9Q LOSS MUTATED              1           8          6
  9Q LOSS WILD-TYPE            7          32         34
D58V36, multiclass
              clus
vv             9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CURRENT USER               1                 7
  FORMER USER                8                32
  NEVER USED                 6                34
[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
D58V38, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   11  2
  9Q LOSS WILD-TYPE 62 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     11    2
  9Q LOSS WILD-TYPE   62   12
         clus
vv        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ABSENT               11                62
  PRESENT               2                12
[1] 2 2
[1] FALSE
D58V39, continuous
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  9Q LOSS MUTATED     0    1   1   10    1  0   1    0    1   2   1  0  1
  9Q LOSS WILD-TYPE   2    0  21   41   20  3   5    6    7  11   1  1  6
D58V40, multiclass
      clus
vv     9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1A                0                 2
  T1A1               1                 0
  T1B                1                21
  T1B1              10                41
  T1B2               1                20
  T2                 0                 3
  T2A                1                 5
  T2A1               0                 6
  T2A2               1                 7
  T2B                2                11
  T3B                1                 1
  T4                 0                 1
  TX                 1                 6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V41, continuous

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    27   9
  10P LOSS WILD-TYPE 110  23
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                133 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 9                 23 
$`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-A1MN TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
       35.61         0.46        40.93        73.18        73.45        83.05 
TCGA-C5-A7CG TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7X8 TCGA-EA-A3QD TCGA-EA-A439 
      182.93         9.67        73.41         2.73        13.05        14.50 
TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 
       14.89        14.96         0.36         2.24         0.10        20.35 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A40J TCGA-HM-A3JK TCGA-IR-A3LB TCGA-IR-A3LH 
        1.22         0.92         1.35        20.78        66.81        78.71 
TCGA-JW-A5VK TCGA-LP-A4AX TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-UC-A7PF 
       20.48         0.07         2.96         3.45         3.39        93.99 

$`10P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        57.04        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
      177.04       173.29         5.46        67.46        46.32        30.21 
TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS 
       35.01        57.73        53.16         2.43         3.58        44.22 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43         0.82        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        25.35       101.82       134.33        15.48 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 
       17.19        85.55        60.69        94.95         9.34        13.61 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       87.75        58.88        36.76         2.66       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE 
       12.36         1.74         1.32         0.82         0.62         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
       14.50         1.35         1.35         1.81        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX 
        0.26         1.48        13.91         0.69        14.99        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RO 
        0.07         4.04         0.03         1.18        23.70         0.07 
TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.10         0.03         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        4.47         6.12        23.84         2.17         0.66         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G 
        1.45         1.58         1.48         0.82         3.52         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.97         1.12        25.41        21.67        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK 
      147.39       137.16       117.40        96.95        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       36.36        14.43        16.64        19.33        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        5.13         0.10         0.89         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 
        5.42        29.72         0.07         4.34         3.72         5.85 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD 
       11.67 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            182.93             177.04 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             17.41              12.66 
[1] "0.1 - 182.9 (17.4)" "0.0 - 177.0 (12.7)"
[1] "hr=" "1.3"
D59V2, continuous
                    vv
clus                 T1 T2+T3+T4
  10P LOSS MUTATED   17       11
  10P LOSS WILD-TYPE 80       28
D59V3, multiclass
          clus
vv         10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                     17                 80
  T2+T3+T4               11                 28
[1] 2 2
[1] FALSE
D59V4, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   13 13
  10P LOSS WILD-TYPE 74 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     13   13
  10P LOSS WILD-TYPE   74   27
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               13                 74
  1               13                 27
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10P LOSS MUTATED   13  0 16
  10P LOSS WILD-TYPE 59  3 49
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               13                 59
  M1                0                  3
  MX               16                 49
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED               0                               33
  10P LOSS WILD-TYPE             2                              111
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10P LOSS MUTATED                                               1
  10P LOSS WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10P LOSS MUTATED                                     3
  10P LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10P LOSS MUTATED                                           1
  10P LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10P LOSS MUTATED                                              1
  10P LOSS WILD-TYPE                                            3
D59V6, multiclass
                                               clus
vv                                              10P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            33
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              10P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             111
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    10  29
  10P LOSS WILD-TYPE  17 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     10   29
  10P LOSS WILD-TYPE   17  120
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                10                 17
  YES               29                120
[1] 2 2
[1] FALSE
D59V8, continuous
D59V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     3
  10P LOSS WILD-TYPE                                7    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED                           7
  10P LOSS WILD-TYPE                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           0    28
  10P LOSS WILD-TYPE                                         1   102
D59V10, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    3                 12
  BLACK OR AFRICAN AMERICAN                                7                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   28                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"
D59V11, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1 29
  10P LOSS WILD-TYPE 10 98
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   29
  10P LOSS WILD-TYPE   10   98
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               29                 98
[1] 2 2
[1] FALSE
D59V12, continuous
D59V13, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   14  5
  10P LOSS WILD-TYPE 34 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     14    5
  10P LOSS WILD-TYPE   34   14
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  TUMOR FREE               14                 34
  WITH TUMOR                5                 14
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  10P LOSS MUTATED         1      1       0            34       3
  10P LOSS WILD-TYPE       0      9       6           113       9
D59V14, multiclass
               clus
vv              10P LOSS MUTATED 10P LOSS WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES               34                113
  VIETNAM                      3                  9
[1] 5 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                 G1 G2 G3 G4 GX
  10P LOSS MUTATED    0 16 21  1  1
  10P LOSS WILD-TYPE 14 67 51  0  4
D59V15, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  G1                0                 14
  G2               16                 67
  G3               21                 51
  G4                1                  0
  GX                1                  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"
D59V16, continuous
D59V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10P LOSS MUTATED                                             6
  10P LOSS WILD-TYPE                                          15
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  10P LOSS MUTATED                                        4
  10P LOSS WILD-TYPE                                      4
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  10P LOSS MUTATED                                                 0
  10P LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10P LOSS MUTATED                9                  12
  10P LOSS WILD-TYPE             27                  71
D59V18, multiclass
                                                 clus
vv                                                10P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    6
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 9
  LIFELONG NON-SMOKER                                           12
                                                 clus
vv                                                10P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     15
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  27
  LIFELONG NON-SMOKER                                             71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  10P LOSS MUTATED             6        8             3        1
  10P LOSS WILD-TYPE          11       29             8        4
D59V20, multiclass
               clus
vv              10P LOSS MUTATED 10P LOSS WILD-TYPE
  COMBINATION                  6                 11
  EXTERNAL                     8                 29
  EXTERNAL BEAM                3                  8
  INTERNAL                     1                  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"
D59V21, binary
                    cls
clus                 0 1
  10P LOSS MUTATED   4 0
  10P LOSS WILD-TYPE 7 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    0
  10P LOSS WILD-TYPE    7    3
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  CGY                4                  7
  GY                 0                  3
[1] 2 2
[1] FALSE
D59V22, continuous
D59V23, continuous
D59V24, continuous
D59V25, continuous
D59V26, continuous
D59V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  10P LOSS MUTATED                                     0
  10P LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  10P LOSS MUTATED                                     3
  10P LOSS WILD-TYPE                                   3
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  10P LOSS MUTATED                         1                       0
  10P LOSS WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10P LOSS MUTATED                         3
  10P LOSS WILD-TYPE                       2
D59V28, multiclass
                                     clus
vv                                    10P LOSS MUTATED 10P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                3                  3
  OTHER LOCATION, SPECIFY                            1                  8
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  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)
  10P LOSS MUTATED                                               0
  10P LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  10P LOSS MUTATED                                                4
  10P LOSS WILD-TYPE                                              6
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10P LOSS MUTATED                                                                                  16
  10P LOSS WILD-TYPE                                                                                38
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10P LOSS MUTATED                                                                                             13
  10P LOSS WILD-TYPE                                                                                           64
D59V29, multiclass
                                                                                              clus
vv                                                                                             10P 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)                          16
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               13
                                                                                              clus
vv                                                                                             10P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                6
  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)                 64
[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"
D59V30, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    7 17
  10P LOSS WILD-TYPE 47 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7   17
  10P LOSS WILD-TYPE   47   42
         clus
vv        10P LOSS MUTATED 10P LOSS WILD-TYPE
  ABSENT                 7                 47
  PRESENT               17                 42
[1] 2 2
[1] FALSE
D59V31, continuous
D59V32, continuous
D59V33, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   11 13
  10P LOSS WILD-TYPE 24 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     11   13
  10P LOSS WILD-TYPE   24   68
                                          clus
vv                                         10P LOSS MUTATED 10P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   11                 24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               13                 68
[1] 2 2
[1] FALSE
D59V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  10P LOSS MUTATED       1                   24                   1
  10P LOSS WILD-TYPE     2                   89                   4
D59V35, multiclass
                      clus
vv                     10P LOSS MUTATED 10P LOSS WILD-TYPE
  OTHER                               1                  2
  RADICAL HYSTERECTOMY               24                 89
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10P LOSS MUTATED              1           9          7
  10P LOSS WILD-TYPE            7          31         33
D59V36, multiclass
              clus
vv             10P LOSS MUTATED 10P LOSS WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 9                 31
  NEVER USED                  7                 33
[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
D59V38, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   13  4
  10P LOSS WILD-TYPE 60 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     13    4
  10P LOSS WILD-TYPE   60   10
         clus
vv        10P LOSS MUTATED 10P LOSS WILD-TYPE
  ABSENT                13                 60
  PRESENT                4                 10
[1] 2 2
[1] FALSE
D59V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  10P LOSS MUTATED     0    0   4   12    1  2   1    3    1   4   0  0  2
  10P LOSS WILD-TYPE   2    1  18   39   20  1   5    3    7   9   2  1  5
D59V40, multiclass
      clus
vv     10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 4                 18
  T1B1               12                 39
  T1B2                1                 20
  T2                  2                  1
  T2A                 1                  5
  T2A1                3                  3
  T2A2                1                  7
  T2B                 4                  9
  T3B                 0                  2
  T4                  0                  1
  TX                  2                  5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V41, continuous

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    30  11
  10Q LOSS WILD-TYPE 107  21
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                41                128 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                11                 21 
$`10Q 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-A2LT TCGA-C5-A2LV TCGA-C5-A2LX TCGA-C5-A7CG 
       35.61         0.46        73.18        73.45        83.05       182.93 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DS-A0VK TCGA-EA-A3QD 
        9.67        73.41        13.61         2.73        36.76        13.05 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2RJ 
       14.50        14.89        14.96        13.48        12.59         1.18 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3TQ 
        2.24         0.10        20.35         1.22         0.92         1.58 
TCGA-FU-A40J TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LB TCGA-IR-A3LH TCGA-JW-A5VK 
        1.35        21.67        20.78        66.81        78.71        20.48 
TCGA-JW-A69B TCGA-LP-A4AX TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       10.06         0.07         2.96         3.45         3.39 

$`10Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        57.04        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
      177.04       173.29         5.46        67.46        46.32        30.21 
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-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD 
       44.22        78.35       100.14        38.43         0.82        52.01 
TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       18.02        17.85        20.42        25.35       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
       15.48        17.19        85.55        60.69        94.95         9.34 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       87.75        58.88         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18         7.33         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.74         1.32         0.82         0.62         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A6QX TCGA-EK-A2H0 
        1.48        13.91         0.69        14.99        13.58        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
        6.64         0.53         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
        0.36        23.70         0.07         0.10         0.10         0.03 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23L 
        7.92         6.94        14.70         4.47         6.12        23.84 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TX TCGA-FU-A3WB 
        2.17         0.66         1.02         1.45         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A4S6 
        3.52         1.32         1.97         1.12        25.41        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
        4.11       147.39       137.16       117.40        96.95        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       26.56        36.36        14.43        16.64        19.33        15.58 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        5.13         0.10         0.89         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 
        5.42        29.72         0.07         4.34         3.72         5.85 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            182.93             177.04 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             14.50              12.74 
[1] "0.1 - 182.9 (14.5)" "0.0 - 177.0 (12.7)"
[1] "hr=" "1.7"
D60V2, continuous
                    vv
clus                 T1 T2+T3+T4
  10Q LOSS MUTATED   21       11
  10Q LOSS WILD-TYPE 76       28
D60V3, multiclass
          clus
vv         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                     21                 76
  T2+T3+T4               11                 28
[1] 2 2
[1] FALSE
D60V4, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   13 15
  10Q LOSS WILD-TYPE 74 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     13   15
  10Q LOSS WILD-TYPE   74   25
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               13                 74
  1               15                 25
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED   14  0 19
  10Q LOSS WILD-TYPE 58  3 46
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               14                 58
  M1                0                  3
  MX               19                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED               0                               37
  10Q LOSS WILD-TYPE             2                              107
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  10Q LOSS MUTATED                                               1
  10Q LOSS WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  10Q LOSS MUTATED                                     4
  10Q LOSS WILD-TYPE                                  16
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  10Q LOSS MUTATED                                           1
  10Q LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  10Q LOSS MUTATED                                              1
  10Q LOSS WILD-TYPE                                            3
D60V6, multiclass
                                               clus
vv                                              10Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            37
  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                                              10Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             107
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    10  34
  10Q LOSS WILD-TYPE  17 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     10   34
  10Q LOSS WILD-TYPE   17  115
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                10                 17
  YES               34                115
[1] 2 2
[1] FALSE
D60V8, continuous
D60V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     4
  10Q LOSS WILD-TYPE                                7    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED                          10
  10Q LOSS WILD-TYPE                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           0    30
  10Q LOSS WILD-TYPE                                         1   100
D60V10, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    4                 11
  BLACK OR AFRICAN AMERICAN                               10                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   30                100
[1] 5 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
  10Q LOSS MUTATED    2 34
  10Q LOSS WILD-TYPE  9 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2   34
  10Q LOSS WILD-TYPE    9   93
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               34                 93
[1] 2 2
[1] FALSE
D60V12, continuous
D60V13, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   14  6
  10Q LOSS WILD-TYPE 34 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     14    6
  10Q LOSS WILD-TYPE   34   13
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  TUMOR FREE               14                 34
  WITH TUMOR                6                 13
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  10Q LOSS MUTATED         1      1       0            38       4
  10Q LOSS WILD-TYPE       0      9       6           109       8
D60V14, multiclass
               clus
vv              10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES               38                109
  VIETNAM                      4                  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                 G1 G2 G3 G4 GX
  10Q LOSS MUTATED    0 16 25  1  2
  10Q LOSS WILD-TYPE 14 67 47  0  3
D60V15, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  G1                0                 14
  G2               16                 67
  G3               25                 47
  G4                1                  0
  GX                2                  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"
D60V16, continuous
D60V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  10Q LOSS MUTATED                                             7
  10Q LOSS WILD-TYPE                                          14
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  10Q LOSS MUTATED                                        4
  10Q LOSS WILD-TYPE                                      4
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  10Q LOSS MUTATED                                                 0
  10Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  10Q LOSS MUTATED                8                  14
  10Q LOSS WILD-TYPE             28                  69
D60V18, multiclass
                                                 clus
vv                                                10Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 8
  LIFELONG NON-SMOKER                                           14
                                                 clus
vv                                                10Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  28
  LIFELONG NON-SMOKER                                             69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  10Q LOSS MUTATED             5        9             5        1
  10Q LOSS WILD-TYPE          12       28             6        4
D60V20, multiclass
               clus
vv              10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COMBINATION                  5                 12
  EXTERNAL                     9                 28
  EXTERNAL BEAM                5                  6
  INTERNAL                     1                  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"
D60V21, binary
                    cls
clus                 0 1
  10Q LOSS MUTATED   5 0
  10Q LOSS WILD-TYPE 6 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    0
  10Q LOSS WILD-TYPE    6    3
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CGY                5                  6
  GY                 0                  3
[1] 2 2
[1] FALSE
D60V22, continuous
D60V23, continuous
D60V24, continuous
D60V25, continuous
D60V26, continuous
D60V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  10Q LOSS MUTATED                                     0
  10Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  10Q LOSS MUTATED                                     3
  10Q LOSS WILD-TYPE                                   3
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  10Q LOSS MUTATED                         1                       0
  10Q LOSS WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  10Q LOSS MUTATED                         4
  10Q LOSS WILD-TYPE                       1
D60V28, multiclass
                                     clus
vv                                    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                3                  3
  OTHER LOCATION, SPECIFY                            1                  8
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            4                  1
[1] 5 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                                                5
  10Q LOSS WILD-TYPE                                              5
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  10Q LOSS MUTATED                                                                                  18
  10Q LOSS WILD-TYPE                                                                                36
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  10Q LOSS MUTATED                                                                                             13
  10Q LOSS WILD-TYPE                                                                                           64
D60V29, multiclass
                                                                                              clus
vv                                                                                             10Q LOSS 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)               13
                                                                                              clus
vv                                                                                             10Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                5
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            36
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 64
[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"
D60V30, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    7 20
  10Q LOSS WILD-TYPE 47 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      7   20
  10Q LOSS WILD-TYPE   47   39
         clus
vv        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ABSENT                 7                 47
  PRESENT               20                 39
[1] 2 2
[1] FALSE
D60V31, continuous
D60V32, continuous
D60V33, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   11 18
  10Q LOSS WILD-TYPE 24 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     11   18
  10Q LOSS WILD-TYPE   24   63
                                          clus
vv                                         10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   11                 24
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               18                 63
[1] 2 2
[1] FALSE
D60V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  10Q LOSS MUTATED       1                   28                   1
  10Q LOSS WILD-TYPE     2                   85                   4
D60V35, multiclass
                      clus
vv                     10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  OTHER                               1                  2
  RADICAL HYSTERECTOMY               28                 85
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  10Q LOSS MUTATED              1           9          9
  10Q LOSS WILD-TYPE            7          31         31
D60V36, multiclass
              clus
vv             10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 9                 31
  NEVER USED                  9                 31
[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, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   14  4
  10Q LOSS WILD-TYPE 59 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     14    4
  10Q LOSS WILD-TYPE   59   10
         clus
vv        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ABSENT                14                 59
  PRESENT                4                 10
[1] 2 2
[1] FALSE
D60V39, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                  7 
        TCGA-C5-A1BN         TCGA-C5-A1MN         TCGA-C5-A1MP 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-JW-A852         TCGA-MU-A51Y 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-MU-A8JM 
"10Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  10Q LOSS MUTATED     0    0   4   14    3  2   1    3    0   5   0  0  2
  10Q LOSS WILD-TYPE   2    1  18   37   18  1   5    3    8   8   2  1  5
D60V40, multiclass
      clus
vv     10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 4                 18
  T1B1               14                 37
  T1B2                3                 18
  T2                  2                  1
  T2A                 1                  5
  T2A1                3                  3
  T2A2                0                  8
  T2B                 5                  8
  T3B                 0                  2
  T4                  0                  1
  TX                  2                  5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V41, continuous

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   42 12
  11P LOSS WILD-TYPE 95 20
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                54                115 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                12                 20 
$`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-A2LV TCGA-C5-A2LZ 
       30.21        38.99        35.61         0.46        73.45       100.14 
TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X8 TCGA-DR-A0ZL 
      182.93        25.35        60.69        94.95         2.73        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A411 
       36.76         2.66       117.99       118.65        12.36         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A50E TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.50         1.81        12.66         0.26        14.99        14.96 
TCGA-EK-A2PG TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI 
        0.53         2.24         0.10        20.35        23.84         1.45 
TCGA-FU-A3WB TCGA-IR-A3LA TCGA-IR-A3LC TCGA-IR-A3LK TCGA-JW-A5VI TCGA-JW-A5VJ 
        0.82       137.16       117.40        26.56        16.64        19.33 
TCGA-JW-A5VK TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MY-A5BD 
       20.48         0.10         0.07         0.82        13.87        29.72 
TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PD 
        0.07         2.96         3.45         3.39        19.59        11.67 

$`11P LOSS WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ 
       57.04        23.67        11.44        68.84        36.56       144.16 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M9 TCGA-C5-A1ME 
      173.29        82.85         5.46        67.46        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       53.16         2.43        40.93         3.58        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       83.05        78.35        38.43         0.82        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         9.67 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZM 
       73.41        17.19        85.55         9.34        13.61        58.88 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       14.50         1.35        12.82        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
        0.69        13.58        13.48        12.59        45.96         6.64 
TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ 
        0.59         0.07         4.04         0.03         0.36         1.18 
TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
       23.70         0.10         0.07         0.10         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG 
        6.94        14.70         4.47         6.12         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3YQ 
        2.17         0.66         1.02         1.58         1.48         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.35         1.32         1.97         1.12        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LB TCGA-IR-A3LF 
       20.78        14.93         4.11       147.39        66.81        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VL TCGA-JW-A69B 
       78.71        81.96        36.36        14.43        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AW TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BF TCGA-Q1-A5R1 
        5.13         0.89         0.03         5.42         4.34         3.72 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 
        5.85         3.72         5.75         4.80         6.25         3.88 
TCGA-UC-A7PF 
       93.99 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            182.93             173.29 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            19.035             10.060 
[1] "0.1 - 182.9 (19.0)" "0.0 - 173.3 (10.1)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 T1 T2+T3+T4
  11P LOSS MUTATED   31       14
  11P LOSS WILD-TYPE 66       25
D61V3, multiclass
          clus
vv         11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                     31                 66
  T2+T3+T4               14                 25
[1] 2 2
[1] FALSE
D61V4, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   31 11
  11P LOSS WILD-TYPE 56 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     31   11
  11P LOSS WILD-TYPE   56   29
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               31                 56
  1               11                 29
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED   27  0 20
  11P LOSS WILD-TYPE 45  3 45
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               27                 45
  M1                0                  3
  MX               20                 45
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED               0                               55
  11P LOSS WILD-TYPE             2                               89
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11P LOSS MUTATED                                               0
  11P LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11P LOSS MUTATED                                     2
  11P LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11P LOSS MUTATED                                           1
  11P LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11P LOSS MUTATED                                              1
  11P LOSS WILD-TYPE                                            3
D61V6, multiclass
                                               clus
vv                                              11P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            55
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              11P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                              89
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D61V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    7 52
  11P LOSS WILD-TYPE 20 97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      7   52
  11P LOSS WILD-TYPE   20   97
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 7                 20
  YES               52                 97
[1] 2 2
[1] FALSE
D61V8, continuous
D61V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  3     9
  11P LOSS WILD-TYPE                                4     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED                           8
  11P LOSS WILD-TYPE                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           1    38
  11P LOSS WILD-TYPE                                         0    92
D61V10, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  4
  ASIAN                                                    9                  6
  BLACK OR AFRICAN AMERICAN                                8                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   38                 92
[1] 5 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
  11P LOSS MUTATED    4 41
  11P LOSS WILD-TYPE  7 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4   41
  11P LOSS WILD-TYPE    7   86
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  7
  NOT HISPANIC OR LATINO               41                 86
[1] 2 2
[1] FALSE
D61V12, continuous
D61V13, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   16  9
  11P LOSS WILD-TYPE 32 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     16    9
  11P LOSS WILD-TYPE   32   10
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  TUMOR FREE               16                 32
  WITH TUMOR                9                 10
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  11P LOSS MUTATED         1      2       2            46       8
  11P LOSS WILD-TYPE       0      8       4           101       4
D61V14, multiclass
               clus
vv              11P LOSS MUTATED 11P LOSS WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       2                  8
  UKRAINE                      2                  4
  UNITED STATES               46                101
  VIETNAM                      8                  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                 G1 G2 G3 G4 GX
  11P LOSS MUTATED    2 24 31  0  1
  11P LOSS WILD-TYPE 12 59 41  1  4
D61V15, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  G1                2                 12
  G2               24                 59
  G3               31                 41
  G4                0                  1
  GX                1                  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"
D61V16, continuous
D61V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11P LOSS MUTATED                                             4
  11P LOSS WILD-TYPE                                          17
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  11P LOSS MUTATED                                        2
  11P LOSS WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  11P LOSS MUTATED                                                 0
  11P LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11P LOSS MUTATED               11                  35
  11P LOSS WILD-TYPE             25                  48
D61V18, multiclass
                                                 clus
vv                                                11P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                11
  LIFELONG NON-SMOKER                                           35
                                                 clus
vv                                                11P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  25
  LIFELONG NON-SMOKER                                             48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  11P LOSS MUTATED             4       12             3        2
  11P LOSS WILD-TYPE          13       25             8        3
D61V20, multiclass
               clus
vv              11P LOSS MUTATED 11P LOSS WILD-TYPE
  COMBINATION                  4                 13
  EXTERNAL                    12                 25
  EXTERNAL BEAM                3                  8
  INTERNAL                     2                  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"
D61V21, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    1  1
  11P LOSS WILD-TYPE 10  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    1
  11P LOSS WILD-TYPE   10    2
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  CGY                1                 10
  GY                 1                  2
[1] 2 2
[1] FALSE
D61V22, continuous
D61V23, continuous
D61V24, continuous
D61V25, continuous
D61V26, continuous
D61V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  11P LOSS MUTATED                                     0
  11P LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  11P LOSS MUTATED                                     2
  11P LOSS WILD-TYPE                                   4
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  11P LOSS MUTATED                         4                       1
  11P LOSS WILD-TYPE                       5                       0
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11P LOSS MUTATED                         1
  11P LOSS WILD-TYPE                       4
D61V28, multiclass
                                     clus
vv                                    11P LOSS MUTATED 11P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  4
  OTHER LOCATION, SPECIFY                            4                  5
  POSITIVE BLADDER MARGIN                            1                  0
  POSITIVE VAGINAL MARGIN                            1                  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)
  11P LOSS MUTATED                                               1
  11P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  11P LOSS MUTATED                                                5
  11P LOSS WILD-TYPE                                              5
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11P LOSS MUTATED                                                                                  23
  11P LOSS WILD-TYPE                                                                                31
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11P LOSS MUTATED                                                                                             19
  11P LOSS WILD-TYPE                                                                                           58
D61V29, multiclass
                                                                                              clus
vv                                                                                             11P 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)                          23
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               19
                                                                                              clus
vv                                                                                             11P LOSS WILD-TYPE
  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)                            31
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 58
[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"
D61V30, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   17 18
  11P LOSS WILD-TYPE 37 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     17   18
  11P LOSS WILD-TYPE   37   41
         clus
vv        11P LOSS MUTATED 11P LOSS WILD-TYPE
  ABSENT                17                 37
  PRESENT               18                 41
[1] 2 2
[1] FALSE
D61V31, continuous
D61V32, continuous
D61V33, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   14 27
  11P LOSS WILD-TYPE 21 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     14   27
  11P LOSS WILD-TYPE   21   54
                                          clus
vv                                         11P LOSS MUTATED 11P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   14                 21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               27                 54
[1] 2 2
[1] FALSE
D61V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  11P LOSS MUTATED       0                   37                   3
  11P LOSS WILD-TYPE     3                   76                   2
D61V35, multiclass
                      clus
vv                     11P LOSS MUTATED 11P LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               37                 76
  SIMPLE HYSTERECTOMY                 3                  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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11P LOSS MUTATED              1          13         16
  11P LOSS WILD-TYPE            7          27         24
D61V36, multiclass
              clus
vv             11P LOSS MUTATED 11P LOSS WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                13                 27
  NEVER USED                 16                 24
[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, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   25  5
  11P LOSS WILD-TYPE 48  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     25    5
  11P LOSS WILD-TYPE   48    9
         clus
vv        11P LOSS MUTATED 11P LOSS WILD-TYPE
  ABSENT                25                 48
  PRESENT                5                  9
[1] 2 2
[1] FALSE
D61V39, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                  7 
        TCGA-C5-A1BN         TCGA-C5-A1MN         TCGA-C5-A1MP 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-MU-A8JM 
"11P LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  11P LOSS MUTATED     1    0   9   18    3  1   1    3    2   6   0  1  3
  11P LOSS WILD-TYPE   1    1  13   33   18  2   5    3    6   7   2  0  4
D61V40, multiclass
      clus
vv     11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1A                 1                  1
  T1A1                0                  1
  T1B                 9                 13
  T1B1               18                 33
  T1B2                3                 18
  T2                  1                  2
  T2A                 1                  5
  T2A1                3                  3
  T2A2                2                  6
  T2B                 6                  7
  T3B                 0                  2
  T4                  1                  0
  TX                  3                  4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V41, continuous

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   53 13
  11Q LOSS WILD-TYPE 84 19
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                66                103 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                13                 19 
$`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-A2LV 
       53.16        38.99        35.61         0.46         2.43        73.45 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CM TCGA-C5-A7UH 
      100.14         0.82       182.93        25.35         9.67        60.69 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
        2.73        87.75        36.76         2.66       117.99       118.65 
TCGA-DS-A5RQ TCGA-EA-A1QT TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A50E 
       16.83        12.36         1.35        14.50         1.81         0.26 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RD 
       14.99        14.96        13.48        12.59         0.53         0.03 
TCGA-EK-A2RM TCGA-EK-A3GJ TCGA-EX-A1H5 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A3NI 
        2.24         0.10        20.35         4.47         6.12         1.45 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LI 
        1.58         0.82       137.16        66.81       117.40        81.96 
TCGA-JW-A5VK TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
       20.48         0.10         0.07         0.82        13.87         0.03 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       29.72         0.07         4.34         2.96         3.45         3.39 
TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        5.75         4.80        19.59         3.88        11.67        93.99 

$`11Q LOSS WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       57.04        23.67        11.44        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M9 
      173.29        82.85         5.46        19.86        67.46        35.01 
TCGA-C5-A1ME TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX 
       57.73        40.93         3.58        44.22        73.18        83.05 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
       78.35        38.43        52.01        18.02        17.85        20.42 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48        73.41        17.19        85.55 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZM TCGA-DS-A3LQ TCGA-DS-A7WF 
       94.95         9.34        13.61        58.88        22.98        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        7.33         8.28         0.76         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A44S 
        0.62        13.05         1.18        14.50         1.35        12.66 
TCGA-EA-A4BA TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A6QX 
       12.82        14.89         1.48        13.91         0.69        13.58 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE 
       45.96         6.64         0.59         0.07         4.04         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN 
        1.18        23.70         0.10         0.07         0.10         0.03 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        7.92         6.94        14.70         1.22        23.84         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3YQ TCGA-FU-A40J 
        2.17         0.66         1.02         1.48         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         1.12        25.41        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LK 
       14.93         4.11       147.39        96.95        78.71        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       36.36        14.43        16.64        19.33        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AW TCGA-MU-A8JM TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV 
        5.13         0.89         5.42         3.72         5.85         3.72 
TCGA-Q1-A73R 
        6.25 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.03               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            182.93             177.04 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            13.035             13.610 
[1] "0.0 - 182.9 (13.0)" "0.0 - 177.0 (13.6)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 T1 T2+T3+T4
  11Q LOSS MUTATED   38       13
  11Q LOSS WILD-TYPE 59       26
D62V3, multiclass
          clus
vv         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                     38                 59
  T2+T3+T4               13                 26
[1] 2 2
[1] FALSE
D62V4, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   34 14
  11Q LOSS WILD-TYPE 53 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     34   14
  11Q LOSS WILD-TYPE   53   26
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               34                 53
  1               14                 26
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED   29  1 24
  11Q LOSS WILD-TYPE 43  2 41
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               29                 43
  M1                1                  2
  MX               24                 41
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED               0                               61
  11Q LOSS WILD-TYPE             2                               83
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  11Q LOSS MUTATED                                               1
  11Q LOSS WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  11Q LOSS MUTATED                                     5
  11Q LOSS WILD-TYPE                                  15
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  11Q LOSS MUTATED                                           1
  11Q LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  11Q LOSS MUTATED                                              1
  11Q LOSS WILD-TYPE                                            3
D62V6, multiclass
                                               clus
vv                                              11Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            61
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          5
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              11Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                              83
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           15
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D62V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   10 59
  11Q LOSS WILD-TYPE 17 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     10   59
  11Q LOSS WILD-TYPE   17   90
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                10                 17
  YES               59                 90
[1] 2 2
[1] FALSE
D62V8, continuous
D62V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  2    10
  11Q LOSS WILD-TYPE                                5     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED                           8
  11Q LOSS WILD-TYPE                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           1    47
  11Q LOSS WILD-TYPE                                         0    83
D62V10, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  5
  ASIAN                                                   10                  5
  BLACK OR AFRICAN AMERICAN                                8                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   47                 83
[1] 5 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
  11Q LOSS MUTATED    2 51
  11Q LOSS WILD-TYPE  9 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   51
  11Q LOSS WILD-TYPE    9   76
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               51                 76
[1] 2 2
[1] FALSE
D62V12, continuous
D62V13, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   18  9
  11Q LOSS WILD-TYPE 30 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     18    9
  11Q LOSS WILD-TYPE   30   10
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  TUMOR FREE               18                 30
  WITH TUMOR                9                 10
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  11Q LOSS MUTATED         1      2       1            57       8
  11Q LOSS WILD-TYPE       0      8       5            90       4
D62V14, multiclass
               clus
vv              11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       2                  8
  UKRAINE                      1                  5
  UNITED STATES               57                 90
  VIETNAM                      8                  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                 G1 G2 G3 G4 GX
  11Q LOSS MUTATED    4 32 30  0  3
  11Q LOSS WILD-TYPE 10 51 42  1  2
D62V15, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  G1                4                 10
  G2               32                 51
  G3               30                 42
  G4                0                  1
  GX                3                  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"
D62V16, continuous
D62V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  11Q LOSS MUTATED                                             9
  11Q LOSS WILD-TYPE                                          12
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  11Q LOSS MUTATED                                        5
  11Q LOSS WILD-TYPE                                      3
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  11Q LOSS MUTATED                                                 0
  11Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  11Q LOSS MUTATED               12                  34
  11Q LOSS WILD-TYPE             24                  49
D62V18, multiclass
                                                 clus
vv                                                11Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    9
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                12
  LIFELONG NON-SMOKER                                           34
                                                 clus
vv                                                11Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     12
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  24
  LIFELONG NON-SMOKER                                             49
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  11Q LOSS MUTATED             7       11             3        3
  11Q LOSS WILD-TYPE          10       26             8        2
D62V20, multiclass
               clus
vv              11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COMBINATION                  7                 10
  EXTERNAL                    11                 26
  EXTERNAL BEAM                3                  8
  INTERNAL                     3                  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"
D62V21, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    1  2
  11Q LOSS WILD-TYPE 10  1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1    2
  11Q LOSS WILD-TYPE   10    1
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CGY                1                 10
  GY                 2                  1
[1] 2 2
[1] FALSE
D62V22, continuous
D62V23, continuous
D62V24, continuous
D62V25, continuous
D62V26, continuous
D62V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  11Q LOSS MUTATED                                     0
  11Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  11Q LOSS MUTATED                                     2
  11Q LOSS WILD-TYPE                                   4
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  11Q LOSS MUTATED                         5                       1
  11Q LOSS WILD-TYPE                       4                       0
                    vv
clus                 POSITIVE VAGINAL MARGIN
  11Q LOSS MUTATED                         1
  11Q LOSS WILD-TYPE                       4
D62V28, multiclass
                                     clus
vv                                    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  4
  OTHER LOCATION, SPECIFY                            5                  4
  POSITIVE BLADDER MARGIN                            1                  0
  POSITIVE VAGINAL MARGIN                            1                  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)
  11Q LOSS MUTATED                                               1
  11Q LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  11Q LOSS MUTATED                                                7
  11Q LOSS WILD-TYPE                                              3
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  11Q LOSS MUTATED                                                                                  29
  11Q LOSS WILD-TYPE                                                                                25
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  11Q LOSS MUTATED                                                                                             22
  11Q LOSS WILD-TYPE                                                                                           55
D62V29, multiclass
                                                                                              clus
vv                                                                                             11Q 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)                          29
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               22
                                                                                              clus
vv                                                                                             11Q LOSS WILD-TYPE
  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)                            25
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 55
[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"
D62V30, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   17 27
  11Q LOSS WILD-TYPE 37 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     17   27
  11Q LOSS WILD-TYPE   37   32
         clus
vv        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ABSENT                17                 37
  PRESENT               27                 32
[1] 2 2
[1] FALSE
D62V31, continuous
D62V32, continuous
D62V33, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   15 32
  11Q LOSS WILD-TYPE 20 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     15   32
  11Q LOSS WILD-TYPE   20   49
                                          clus
vv                                         11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   15                 20
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               32                 49
[1] 2 2
[1] FALSE
D62V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  11Q LOSS MUTATED       2                   41                   3
  11Q LOSS WILD-TYPE     1                   72                   2
D62V35, multiclass
                      clus
vv                     11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  OTHER                               2                  1
  RADICAL HYSTERECTOMY               41                 72
  SIMPLE HYSTERECTOMY                 3                  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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  11Q LOSS MUTATED              1          15         17
  11Q LOSS WILD-TYPE            7          25         23
D62V36, multiclass
              clus
vv             11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                15                 25
  NEVER USED                 17                 23
[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, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   28  7
  11Q LOSS WILD-TYPE 45  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     28    7
  11Q LOSS WILD-TYPE   45    7
         clus
vv        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ABSENT                28                 45
  PRESENT                7                  7
[1] 2 2
[1] FALSE
D62V39, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                  7 
        TCGA-C5-A1BN         TCGA-C5-A1MN         TCGA-C5-A1MP 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-MU-A8JM 
"11Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  11Q LOSS MUTATED     1    1   9   23    4  1   1    2    2   6   0  1  4
  11Q LOSS WILD-TYPE   1    0  13   28   17  2   5    4    6   7   2  0  3
D62V40, multiclass
      clus
vv     11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1A                 1                  1
  T1A1                1                  0
  T1B                 9                 13
  T1B1               23                 28
  T1B2                4                 17
  T2                  1                  2
  T2A                 1                  5
  T2A1                2                  4
  T2A2                2                  6
  T2B                 6                  7
  T3B                 0                  2
  T4                  1                  0
  TX                  4                  3
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V41, continuous

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    18   4
  12P LOSS WILD-TYPE 119  28
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                22                147 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 28 
$`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-DS-A0VK TCGA-DS-A0VL TCGA-EA-A1QT 
       38.43        60.69         2.73        36.76         2.66        12.36 
TCGA-EA-A411 TCGA-EA-A43B TCGA-EK-A2PG TCGA-FU-A2QG TCGA-FU-A40J TCGA-IR-A3LH 
        1.35         1.81         0.53         0.92         1.35        78.71 
TCGA-IR-A3LK TCGA-LP-A4AX TCGA-Q1-A5R2 TCGA-Q1-A6DT 
       26.56         0.07         3.45         3.39 

$`12P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
       36.56       144.16        82.85         5.46        19.86        67.46 
TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       31.40        46.32        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX 
        0.46         2.43         3.58        44.22        73.18        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35       100.14         0.82        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       182.93        25.35       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 
        9.67        73.41        17.19        85.55        94.95         9.34 
TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       13.61        87.75        58.88       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ 
       16.83        16.18         7.33         8.28         0.76         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
        1.35        14.50        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB 
       13.48        12.59        45.96         6.64         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        23.70         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70         4.47         6.12         1.22 
TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       23.84         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 
        1.48         0.82         3.52         1.32         1.97         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LL 
      137.16        66.81       117.40        96.95        81.96        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       14.43        16.64        19.33        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        5.13         0.10         0.89         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         2.96         3.72 
TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        5.85         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.07               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            177.04             182.93 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             19.46              13.58 
[1] "0.1 - 177.0 (19.5)" "0.0 - 182.9 (13.6)"
[1] "hr=" "1.3"
D63V2, continuous
                    vv
clus                 T1 T2+T3+T4
  12P LOSS MUTATED   14        4
  12P LOSS WILD-TYPE 83       35
D63V3, multiclass
          clus
vv         12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                     14                 83
  T2+T3+T4                4                 35
[1] 2 2
[1] FALSE
D63V4, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   12  6
  12P LOSS WILD-TYPE 75 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12    6
  12P LOSS WILD-TYPE   75   34
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               12                 75
  1                6                 34
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12P LOSS MUTATED   11  0  8
  12P LOSS WILD-TYPE 61  3 57
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               11                 61
  M1                0                  3
  MX                8                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED               0                               20
  12P LOSS WILD-TYPE             2                              124
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12P LOSS MUTATED                                               0
  12P LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12P LOSS MUTATED                                     3
  12P LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12P LOSS MUTATED                                           0
  12P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12P LOSS MUTATED                                              1
  12P LOSS WILD-TYPE                                            3
D63V6, multiclass
                                               clus
vv                                              12P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            20
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              12P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             124
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     4  20
  12P LOSS WILD-TYPE  23 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4   20
  12P LOSS WILD-TYPE   23  129
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 4                 23
  YES               20                129
[1] 2 2
[1] FALSE
D63V8, continuous
D63V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     1
  12P LOSS WILD-TYPE                                7    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED                           4
  12P LOSS WILD-TYPE                        14
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           0    19
  12P LOSS WILD-TYPE                                         1   111
D63V10, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    1                 14
  BLACK OR AFRICAN AMERICAN                                4                 14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   19                111
[1] 5 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
  12P LOSS MUTATED     0  19
  12P LOSS WILD-TYPE  11 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   19
  12P LOSS WILD-TYPE   11  108
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               19                108
[1] 2 2
[1] FALSE
D63V12, continuous
D63V13, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    8  2
  12P LOSS WILD-TYPE 40 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      8    2
  12P LOSS WILD-TYPE   40   17
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  TUMOR FREE                8                 40
  WITH TUMOR                2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  12P LOSS MUTATED         0      2       1            20       1
  12P LOSS WILD-TYPE       1      8       5           127      11
D63V14, multiclass
               clus
vv              12P LOSS MUTATED 12P LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       2                  8
  UKRAINE                      1                  5
  UNITED STATES               20                127
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  12P LOSS MUTATED    0 11 11  1  1
  12P LOSS WILD-TYPE 14 72 61  0  4
D63V15, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  G1                0                 14
  G2               11                 72
  G3               11                 61
  G4                1                  0
  GX                1                  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"
D63V16, continuous
D63V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  12P LOSS MUTATED                                             4
  12P LOSS WILD-TYPE                                          17
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  12P LOSS MUTATED                                        0
  12P LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  12P LOSS MUTATED                                                 0
  12P LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12P LOSS MUTATED                3                  14
  12P LOSS WILD-TYPE             33                  69
D63V18, multiclass
                                                 clus
vv                                                12P 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                                                 3
  LIFELONG NON-SMOKER                                           14
                                                 clus
vv                                                12P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  33
  LIFELONG NON-SMOKER                                             69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  12P LOSS MUTATED             2        4             3        1
  12P LOSS WILD-TYPE          15       33             8        4
D63V20, multiclass
               clus
vv              12P LOSS MUTATED 12P LOSS WILD-TYPE
  COMBINATION                  2                 15
  EXTERNAL                     4                 33
  EXTERNAL BEAM                3                  8
  INTERNAL                     1                  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"
D63V21, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    1  0
  12P LOSS WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    0
  12P LOSS WILD-TYPE   10    3
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D63V22, continuous
D63V23, continuous
D63V24, continuous
D63V25, continuous
D63V26, continuous
D63V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  12P LOSS MUTATED                                     0
  12P LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  12P LOSS MUTATED                                     1
  12P LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  12P LOSS MUTATED                         1                       0
  12P LOSS WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12P LOSS MUTATED                         2
  12P LOSS WILD-TYPE                       3
D63V28, multiclass
                                     clus
vv                                    12P LOSS MUTATED 12P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            1                  8
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  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)
  12P LOSS MUTATED                                               1
  12P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  12P LOSS MUTATED                                                2
  12P LOSS WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12P LOSS MUTATED                                                                                   8
  12P LOSS WILD-TYPE                                                                                46
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12P LOSS MUTATED                                                                                             11
  12P LOSS WILD-TYPE                                                                                           66
D63V29, multiclass
                                                                                              clus
vv                                                                                             12P 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)                           8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               11
                                                                                              clus
vv                                                                                             12P LOSS WILD-TYPE
  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)                            46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 66
[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"
D63V30, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    8  7
  12P LOSS WILD-TYPE 46 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      8    7
  12P LOSS WILD-TYPE   46   52
         clus
vv        12P LOSS MUTATED 12P LOSS WILD-TYPE
  ABSENT                 8                 46
  PRESENT                7                 52
[1] 2 2
[1] FALSE
D63V31, continuous
D63V32, continuous
D63V33, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    6  9
  12P LOSS WILD-TYPE 29 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6    9
  12P LOSS WILD-TYPE   29   72
                                          clus
vv                                         12P LOSS MUTATED 12P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                9                 72
[1] 2 2
[1] FALSE
D63V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  12P LOSS MUTATED       0                   16                   1
  12P LOSS WILD-TYPE     3                   97                   4
D63V35, multiclass
                      clus
vv                     12P LOSS MUTATED 12P LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               16                 97
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12P LOSS MUTATED              0           8          8
  12P LOSS WILD-TYPE            8          32         32
D63V36, multiclass
              clus
vv             12P LOSS MUTATED 12P LOSS WILD-TYPE
  CURRENT USER                0                  8
  FORMER USER                 8                 32
  NEVER USED                  8                 32
[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, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   13  0
  12P LOSS WILD-TYPE 60 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     13    0
  12P LOSS WILD-TYPE   60   14
         clus
vv        12P LOSS MUTATED 12P LOSS WILD-TYPE
  ABSENT                13                 60
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D63V39, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                  8 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MP 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  12P LOSS MUTATED     0    0   5    8    1  0   1    2    0   0   1  0  2
  12P LOSS WILD-TYPE   2    1  17   43   20  3   5    4    8  13   1  1  5
D63V40, multiclass
      clus
vv     12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 5                 17
  T1B1                8                 43
  T1B2                1                 20
  T2                  0                  3
  T2A                 1                  5
  T2A1                2                  4
  T2A2                0                  8
  T2B                 0                 13
  T3B                 1                  1
  T4                  0                  1
  TX                  2                  5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V41, continuous

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     5   2
  12Q LOSS WILD-TYPE 132  30
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 7                162 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 30 
$`12Q LOSS MUTATED`
TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MN TCGA-C5-A7UH TCGA-C5-A7X8 TCGA-EK-A2PG 
       30.21        35.01        40.93        60.69         2.73         0.53 
TCGA-FU-A770 
        1.12 

$`12Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A1MP TCGA-C5-A2LS 
       38.99        35.61         0.46         2.43         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 
        0.82        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO 
       25.35       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL 
       17.19        85.55        94.95         9.34        13.61        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76         2.66       117.99       118.65        22.98 
TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT 
       16.83        16.18         7.33         8.28         0.76        12.36 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         0.26        14.89         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        6.64         0.59         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        23.70         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        4.47         6.12         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.66         1.02         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JJ 
        3.52         1.35         1.32         1.97        25.41        21.67 
TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB 
       20.78        14.93         4.11       147.39       137.16        66.81 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B 
       14.43        16.64        19.33        20.48        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y 
        5.13         0.10         0.89         0.07         0.82        13.87 
TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA 
        0.03         5.42        29.72         0.07         4.34         2.96 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        3.72         3.45         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.53               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             60.69             182.93 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             30.21              13.53 
[1] "0.5 - 60.7 (30.2)"  "0.0 - 182.9 (13.5)"
[1] "hr=" "1.7"
D64V2, continuous
                    vv
clus                 T1 T2+T3+T4
  12Q LOSS MUTATED    2        3
  12Q LOSS WILD-TYPE 95       36
D64V3, multiclass
          clus
vv         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                      2                 95
  T2+T3+T4                3                 36
[1] 2 2
[1] FALSE
D64V4, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  3
  12Q LOSS WILD-TYPE 85 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    3
  12Q LOSS WILD-TYPE   85   37
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                2                 85
  1                3                 37
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12Q LOSS MUTATED    2  0  3
  12Q LOSS WILD-TYPE 70  3 62
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                2                 70
  M1                0                  3
  MX                3                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED               0                                6
  12Q LOSS WILD-TYPE             2                              138
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  12Q LOSS MUTATED                                               1
  12Q LOSS WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  12Q LOSS MUTATED                                     1
  12Q LOSS WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  12Q LOSS MUTATED                                           0
  12Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  12Q LOSS MUTATED                                              1
  12Q LOSS WILD-TYPE                                            3
D64V6, multiclass
                                               clus
vv                                              12Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             6
  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                                              12Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             138
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3   6
  12Q LOSS WILD-TYPE  24 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    6
  12Q LOSS WILD-TYPE   24  143
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 3                 24
  YES                6                143
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                7    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED                           1
  12Q LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0     8
  12Q LOSS WILD-TYPE                                         1   122
D64V10, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    0                 15
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    8                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"
D64V11, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0   7
  12Q LOSS WILD-TYPE  11 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    7
  12Q LOSS WILD-TYPE   11  120
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                7                120
[1] 2 2
[1] FALSE
D64V12, continuous
D64V13, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  1
  12Q LOSS WILD-TYPE 46 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    1
  12Q LOSS WILD-TYPE   46   18
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  TUMOR FREE                2                 46
  WITH TUMOR                1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  12Q LOSS MUTATED         0      0       0             9       0
  12Q LOSS WILD-TYPE       1     10       6           138      12
D64V14, multiclass
               clus
vv              12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      0                  6
  UNITED STATES                9                138
  VIETNAM                      0                 12
[1] 5 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                 G1 G2 G3 G4 GX
  12Q LOSS MUTATED    0  4  5  0  0
  12Q LOSS WILD-TYPE 14 79 67  1  5
D64V15, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  G1                0                 14
  G2                4                 79
  G3                5                 67
  G4                0                  1
  GX                0                  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"
D64V16, continuous
D64V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  12Q LOSS MUTATED                                             0
  12Q LOSS WILD-TYPE                                          21
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  12Q LOSS MUTATED                                        0
  12Q LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  12Q LOSS MUTATED                                                 0
  12Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  12Q LOSS MUTATED                3                   3
  12Q LOSS WILD-TYPE             33                  80
D64V18, multiclass
                                                 clus
vv                                                12Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 3
  LIFELONG NON-SMOKER                                            3
                                                 clus
vv                                                12Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  33
  LIFELONG NON-SMOKER                                             80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V19, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                 46 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A2LS         TCGA-C5-A2LT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CL         TCGA-C5-A7CO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-DR-A0ZM         TCGA-DS-A5RQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FU-A5XV         TCGA-HM-A4S6         TCGA-HM-A6W2 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VK         TCGA-MU-A5YI 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-UC-A7PD 
"12Q LOSS WILD-TYPE" 
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  12Q LOSS MUTATED             1        1             2        1
  12Q LOSS WILD-TYPE          16       36             9        4
D64V20, multiclass
               clus
vv              12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COMBINATION                  1                 16
  EXTERNAL                     1                 36
  EXTERNAL BEAM                2                  9
  INTERNAL                     1                  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"
D64V21, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    0  0
  12Q LOSS WILD-TYPE 11  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    0
  12Q LOSS WILD-TYPE   11    3
D64V22, continuous
D64V23, continuous
D64V24, continuous
D64V25, continuous
D64V26, continuous
D64V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  12Q LOSS MUTATED                                     0
  12Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  12Q LOSS MUTATED                                     0
  12Q LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  12Q LOSS MUTATED                         0                       0
  12Q LOSS WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  12Q LOSS MUTATED                         0
  12Q LOSS WILD-TYPE                       5
D64V28, multiclass
                    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                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  12Q LOSS MUTATED                                                                                   3
  12Q LOSS WILD-TYPE                                                                                51
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  12Q LOSS MUTATED                                                                                              3
  12Q LOSS WILD-TYPE                                                                                           74
D64V29, 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)                           3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                3
                                                                                              clus
vv                                                                                             12Q LOSS WILD-TYPE
  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)                            51
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 74
[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"
D64V30, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  3
  12Q LOSS WILD-TYPE 52 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    3
  12Q LOSS WILD-TYPE   52   56
         clus
vv        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ABSENT                 2                 52
  PRESENT                3                 56
[1] 2 2
[1] FALSE
D64V31, continuous
D64V32, continuous
D64V33, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  1
  12Q LOSS WILD-TYPE 33 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    1
  12Q LOSS WILD-TYPE   33   80
                                          clus
vv                                         12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    2                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                1                 80
[1] 2 2
[1] FALSE
D64V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  12Q LOSS MUTATED       0                    5                   0
  12Q LOSS WILD-TYPE     3                  108                   5
D64V35, multiclass
                      clus
vv                     12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY                5                108
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  12Q LOSS MUTATED              0           4          1
  12Q LOSS WILD-TYPE            8          36         39
D64V36, multiclass
              clus
vv             12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CURRENT USER                0                  8
  FORMER USER                 4                 36
  NEVER USED                  1                 39
[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
D64V38, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    3  0
  12Q LOSS WILD-TYPE 70 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    0
  12Q LOSS WILD-TYPE   70   14
         clus
vv        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ABSENT                 3                 70
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D64V39, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                  8 
        TCGA-C5-A1BN         TCGA-C5-A1MH         TCGA-C5-A1MP 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  12Q LOSS MUTATED     0    0   1    1    0  0   1    0    1   0   1  0  0
  12Q LOSS WILD-TYPE   2    1  21   50   21  3   5    6    7  13   1  1  7
D64V40, multiclass
      clus
vv     12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 1                 21
  T1B1                1                 50
  T1B2                0                 21
  T2                  0                  3
  T2A                 1                  5
  T2A1                0                  6
  T2A2                1                  7
  T2B                 0                 13
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V41, continuous

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    36   6
  13Q LOSS WILD-TYPE 101  26
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                42                127 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                 26 
$`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        25.35        73.41 
TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-DR-A0ZL TCGA-DS-A0VM TCGA-DS-A0VN 
       85.55        94.95         9.34        87.75       117.99       118.65 
TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A439 TCGA-EK-A2GZ TCGA-EK-A2R7 
       22.98        12.36         1.18        14.50        12.59         0.59 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI 
        0.03         0.36         2.24        20.35        23.84         1.45 
TCGA-FU-A3TQ TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.58         1.97        25.41        14.93         4.11       147.39 
TCGA-JW-A5VK TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-Q1-A6DT TCGA-R2-A69V 
       20.48         0.10         0.89         0.07         3.39        19.59 

$`13Q LOSS WILD-TYPE`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       23.67        11.44        68.84        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 
      173.29         5.46        19.86        67.46        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-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-A7CJ 
       38.43         0.82        17.85        20.42       182.93       101.82 
TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UH TCGA-C5-A7X5 
      134.33        15.48         9.67        17.19        60.69        13.61 
TCGA-C5-A7X8 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A5RQ TCGA-DS-A7WF 
        2.73        58.88        36.76         2.66        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        7.33         8.28         0.76         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
        0.62        13.05        14.50         1.35         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         0.26        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 
        0.69        14.99        14.96        13.58        13.48        45.96 
TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RJ TCGA-EK-A2RL 
        6.64         0.53         0.07         4.04         1.18        23.70 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 
        0.10         0.07         0.10         0.10         0.03         7.92 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG 
        6.94        14.70         4.47         6.12         1.22         0.92 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        2.17         0.66         1.02         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-IR-A3LA 
        1.35         1.32         1.12        21.67        20.78       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL TCGA-JW-A69B 
       36.36        14.43        16.64        19.33        15.58        10.06 
TCGA-JW-A852 TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        5.13         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-RA-A741 TCGA-UC-A7PD 
        3.72         5.75         4.80         6.25         3.88        11.67 
TCGA-UC-A7PF 
       93.99 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.03               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            147.39             182.93 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             19.97              11.67 
[1] "0.0 - 147.4 (20.0)" "0.0 - 182.9 (11.7)"
[1] "hr=" "2"  
D65V2, continuous
                    vv
clus                 T1 T2+T3+T4
  13Q LOSS MUTATED   22       11
  13Q LOSS WILD-TYPE 75       28
D65V3, multiclass
          clus
vv         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                     22                 75
  T2+T3+T4               11                 28
[1] 2 2
[1] FALSE
D65V4, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   21 12
  13Q LOSS WILD-TYPE 66 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     21   12
  13Q LOSS WILD-TYPE   66   28
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               21                 66
  1               12                 28
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED   19  1 15
  13Q LOSS WILD-TYPE 53  2 50
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               19                 53
  M1                1                  2
  MX               15                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED               1                               45
  13Q LOSS WILD-TYPE             1                               99
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  13Q LOSS MUTATED                                               0
  13Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  13Q LOSS MUTATED                                     0
  13Q LOSS WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  13Q LOSS MUTATED                                           0
  13Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  13Q LOSS MUTATED                                              0
  13Q LOSS WILD-TYPE                                            4
D65V6, multiclass
                                               clus
vv                                              13Q LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            45
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          0
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              13Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  1
  CERVICAL SQUAMOUS CELL CARCINOMA                              99
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9  37
  13Q LOSS WILD-TYPE  18 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   37
  13Q LOSS WILD-TYPE   18  112
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 9                 18
  YES               37                112
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     6
  13Q LOSS WILD-TYPE                                6     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED                           6
  13Q LOSS WILD-TYPE                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           0    32
  13Q LOSS WILD-TYPE                                         1    98
D65V10, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  6
  ASIAN                                                    6                  9
  BLACK OR AFRICAN AMERICAN                                6                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   32                 98
[1] 5 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
  13Q LOSS MUTATED    0 38
  13Q LOSS WILD-TYPE 11 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0   38
  13Q LOSS WILD-TYPE   11   89
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               38                 89
[1] 2 2
[1] FALSE
D65V12, continuous
D65V13, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   14  3
  13Q LOSS WILD-TYPE 34 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     14    3
  13Q LOSS WILD-TYPE   34   16
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  TUMOR FREE               14                 34
  WITH TUMOR                3                 16
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  13Q LOSS MUTATED         0      2       0            39       5
  13Q LOSS WILD-TYPE       1      8       6           108       7
D65V14, multiclass
               clus
vv              13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       2                  8
  UKRAINE                      0                  6
  UNITED STATES               39                108
  VIETNAM                      5                  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                 G1 G2 G3 G4 GX
  13Q LOSS MUTATED    2 18 25  0  1
  13Q LOSS WILD-TYPE 12 65 47  1  4
D65V15, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  G1                2                 12
  G2               18                 65
  G3               25                 47
  G4                0                  1
  GX                1                  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"
D65V16, continuous
D65V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  13Q LOSS MUTATED                                             4
  13Q LOSS WILD-TYPE                                          17
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  13Q LOSS MUTATED                                        5
  13Q LOSS WILD-TYPE                                      3
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  13Q LOSS MUTATED                                                 0
  13Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  13Q LOSS MUTATED               12                  17
  13Q LOSS WILD-TYPE             24                  66
D65V18, multiclass
                                                 clus
vv                                                13Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    4
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         5
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                12
  LIFELONG NON-SMOKER                                           17
                                                 clus
vv                                                13Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           3
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  24
  LIFELONG NON-SMOKER                                             66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  13Q LOSS MUTATED             5        8             3        1
  13Q LOSS WILD-TYPE          12       29             8        4
D65V20, multiclass
               clus
vv              13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COMBINATION                  5                 12
  EXTERNAL                     8                 29
  EXTERNAL BEAM                3                  8
  INTERNAL                     1                  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"
D65V21, binary
                    cls
clus                 0 1
  13Q LOSS MUTATED   3 1
  13Q LOSS WILD-TYPE 8 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3    1
  13Q LOSS WILD-TYPE    8    2
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CGY                3                  8
  GY                 1                  2
[1] 2 2
[1] FALSE
D65V22, continuous
D65V23, continuous
D65V24, continuous
D65V25, continuous
D65V26, continuous
D65V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  13Q LOSS MUTATED                                     0
  13Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  13Q LOSS MUTATED                                     1
  13Q LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  13Q LOSS MUTATED                         4                       0
  13Q LOSS WILD-TYPE                       5                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  13Q LOSS MUTATED                         2
  13Q LOSS WILD-TYPE                       3
D65V28, multiclass
                                     clus
vv                                    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            4                  5
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  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)
  13Q LOSS MUTATED                                               0
  13Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  13Q LOSS MUTATED                                                3
  13Q LOSS WILD-TYPE                                              7
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  13Q LOSS MUTATED                                                                                  16
  13Q LOSS WILD-TYPE                                                                                38
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  13Q LOSS MUTATED                                                                                             16
  13Q LOSS WILD-TYPE                                                                                           61
D65V29, multiclass
                                                                                              clus
vv                                                                                             13Q 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)               16
                                                                                              clus
vv                                                                                             13Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                7
  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)                 61
[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"
D65V30, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    9 18
  13Q LOSS WILD-TYPE 45 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   18
  13Q LOSS WILD-TYPE   45   41
         clus
vv        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ABSENT                 9                 45
  PRESENT               18                 41
[1] 2 2
[1] FALSE
D65V31, continuous
D65V32, continuous
D65V33, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    9 23
  13Q LOSS WILD-TYPE 26 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   23
  13Q LOSS WILD-TYPE   26   58
                                          clus
vv                                         13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    9                 26
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               23                 58
[1] 2 2
[1] FALSE
D65V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  13Q LOSS MUTATED       0                   31                   2
  13Q LOSS WILD-TYPE     3                   82                   3
D65V35, multiclass
                      clus
vv                     13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               31                 82
  SIMPLE HYSTERECTOMY                 2                  3
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  13Q LOSS MUTATED              2           9          6
  13Q LOSS WILD-TYPE            6          31         34
D65V36, multiclass
              clus
vv             13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CURRENT USER                2                  6
  FORMER USER                 9                 31
  NEVER USED                  6                 34
[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
D65V38, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   12  6
  13Q LOSS WILD-TYPE 61  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     12    6
  13Q LOSS WILD-TYPE   61    8
         clus
vv        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ABSENT                12                 61
  PRESENT                6                  8
[1] 2 2
[1] FALSE
D65V39, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                  8 
        TCGA-C5-A1BN         TCGA-C5-A1MN         TCGA-C5-A1MP 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  13Q LOSS MUTATED     1    0   5   10    6  3   1    2    1   3   1  0  2
  13Q LOSS WILD-TYPE   1    1  17   41   15  0   5    4    7  10   1  1  5
D65V40, multiclass
      clus
vv     13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1A                 1                  1
  T1A1                0                  1
  T1B                 5                 17
  T1B1               10                 41
  T1B2                6                 15
  T2                  3                  0
  T2A                 1                  5
  T2A1                2                  4
  T2A2                1                  7
  T2B                 3                 10
  T3B                 1                  1
  T4                  0                  1
  TX                  2                  5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V41, continuous

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    16   1
  14Q LOSS WILD-TYPE 121  31
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                17                152 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                 31 
$`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-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2RJ 
        9.67        14.50         1.35         1.81         0.53         1.18 
TCGA-EK-A2RM TCGA-FU-A23L TCGA-FU-A3TX TCGA-LP-A4AU TCGA-Q1-A5R2 
        2.24        23.84         1.48         0.10         3.45 

$`14Q LOSS 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-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-A1M9 TCGA-C5-A1MF 
       67.46        31.40        46.32        30.21        35.01        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-A2LT TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD 
       73.18        73.45        78.35       100.14         0.82        52.01 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       182.93        25.35       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        9.34        13.61         2.73        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
        2.66       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        7.33         8.28         0.76        12.36         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A439 
        0.82         0.62        13.05         1.18         1.35        14.50 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         0.26        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
        0.69        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       45.96         6.64         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.36        23.70         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.12         1.22         0.92         2.17         0.66         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.45         1.58         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AW 
       19.33        20.48        15.58        10.06         5.13         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        0.07         4.34         2.96         3.72         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.10               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             83.05             182.93 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              3.45              13.74 
[1] "0.1 - 83.0 (3.5)"   "0.0 - 182.9 (13.7)"
[1] "hr=" "2.1"
D66V2, continuous
                    vv
clus                 T1 T2+T3+T4
  14Q LOSS MUTATED   10        3
  14Q LOSS WILD-TYPE 87       36
D66V3, multiclass
          clus
vv         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                     10                 87
  T2+T3+T4                3                 36
[1] 2 2
[1] FALSE
D66V4, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   11  2
  14Q LOSS WILD-TYPE 76 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11    2
  14Q LOSS WILD-TYPE   76   38
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               11                 76
  1                2                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED    8  0  6
  14Q LOSS WILD-TYPE 64  3 59
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                8                 64
  M1                0                  3
  MX                6                 59
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED               0                               15
  14Q LOSS WILD-TYPE             2                              129
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  14Q LOSS MUTATED                                               1
  14Q LOSS WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  14Q LOSS MUTATED                                     3
  14Q LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  14Q LOSS MUTATED                                           0
  14Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  14Q LOSS MUTATED                                              0
  14Q LOSS WILD-TYPE                                            4
D66V6, multiclass
                                               clus
vv                                              14Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            15
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              14Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             129
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  18
  14Q LOSS WILD-TYPE  26 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   18
  14Q LOSS WILD-TYPE   26  131
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 1                 26
  YES               18                131
[1] 2 2
[1] FALSE
D66V8, continuous
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1MF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MN 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A2M2         TCGA-C5-A3HD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A7UI         TCGA-C5-A7X8         TCGA-DR-A0ZM 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-EA-A556 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JW-A5VI 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-MU-A5YI         TCGA-MU-A8JM 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741         TCGA-UC-A7PD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
D66V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     1
  14Q LOSS WILD-TYPE                                7    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED                           1
  14Q LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           0    16
  14Q LOSS WILD-TYPE                                         1   114
D66V10, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    1                 14
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                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"
D66V11, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  13
  14Q LOSS WILD-TYPE  10 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   13
  14Q LOSS WILD-TYPE   10  114
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               13                114
[1] 2 2
[1] FALSE
D66V12, continuous
D66V13, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    7  0
  14Q LOSS WILD-TYPE 41 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      7    0
  14Q LOSS WILD-TYPE   41   19
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  TUMOR FREE                7                 41
  WITH TUMOR                0                 19
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  14Q LOSS MUTATED         0      1       2            15       1
  14Q LOSS WILD-TYPE       1      9       4           132      11
D66V14, multiclass
               clus
vv              14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      2                  4
  UNITED STATES               15                132
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  14Q LOSS MUTATED    1  6 12  0  0
  14Q LOSS WILD-TYPE 13 77 60  1  5
D66V15, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  G1                1                 13
  G2                6                 77
  G3               12                 60
  G4                0                  1
  GX                0                  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"
D66V16, continuous
D66V17, continuous
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1MF 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MN 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A2M2         TCGA-C5-A3HD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-C5-A7UI         TCGA-C5-A7X8         TCGA-DR-A0ZM 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-DS-A7WF         TCGA-EA-A556 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JW-A5VI 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-MU-A5YI         TCGA-MU-A8JM 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741         TCGA-UC-A7PD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  14Q LOSS MUTATED                                             3
  14Q LOSS WILD-TYPE                                          18
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  14Q LOSS MUTATED                                        0
  14Q LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  14Q LOSS MUTATED                                                 0
  14Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  14Q LOSS MUTATED                1                   9
  14Q LOSS WILD-TYPE             35                  74
D66V18, multiclass
                                                 clus
vv                                                14Q 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                                                 1
  LIFELONG NON-SMOKER                                            9
                                                 clus
vv                                                14Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  35
  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"
D66V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  14Q LOSS MUTATED             1        5             0        0
  14Q LOSS WILD-TYPE          16       32            11        5
D66V20, multiclass
               clus
vv              14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COMBINATION                  1                 16
  EXTERNAL                     5                 32
  EXTERNAL BEAM                0                 11
  INTERNAL                     0                  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"
D66V21, binary
                    cls
clus                 0 1
  14Q LOSS MUTATED   2 0
  14Q LOSS WILD-TYPE 9 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2    0
  14Q LOSS WILD-TYPE    9    3
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CGY                2                  9
  GY                 0                  3
[1] 2 2
[1] FALSE
D66V22, continuous
D66V23, continuous
D66V24, continuous
D66V25, continuous
D66V26, continuous
D66V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  14Q LOSS MUTATED                                     0
  14Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  14Q LOSS MUTATED                                     1
  14Q LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  14Q LOSS MUTATED                         0                       0
  14Q LOSS WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  14Q LOSS MUTATED                         1
  14Q LOSS WILD-TYPE                       4
D66V28, multiclass
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 2                 21 
        TCGA-C5-A0TN         TCGA-C5-A1BE         TCGA-C5-A1BM 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EK-A2RN         TCGA-EK-A2RO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A8JM         TCGA-UC-A7PD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
                    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                                                0
  14Q LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  14Q LOSS MUTATED                                                                                   8
  14Q LOSS WILD-TYPE                                                                                46
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  14Q LOSS MUTATED                                                                                              5
  14Q LOSS WILD-TYPE                                                                                           72
D66V29, multiclass
                                                                                              clus
vv                                                                                             14Q 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)                           8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                5
                                                                                              clus
vv                                                                                             14Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 72
[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"
D66V30, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    6  5
  14Q LOSS WILD-TYPE 48 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      6    5
  14Q LOSS WILD-TYPE   48   54
         clus
vv        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ABSENT                 6                 48
  PRESENT                5                 54
[1] 2 2
[1] FALSE
D66V31, continuous
D66V32, continuous
D66V33, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    4  8
  14Q LOSS WILD-TYPE 31 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4    8
  14Q LOSS WILD-TYPE   31   73
                                          clus
vv                                         14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    4                 31
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                8                 73
[1] 2 2
[1] FALSE
D66V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  14Q LOSS MUTATED       0                   13                   2
  14Q LOSS WILD-TYPE     3                  100                   3
D66V35, multiclass
                      clus
vv                     14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               13                100
  SIMPLE HYSTERECTOMY                 2                  3
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  14Q LOSS MUTATED              0           5          1
  14Q LOSS WILD-TYPE            8          35         39
D66V36, multiclass
              clus
vv             14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CURRENT USER                0                  8
  FORMER USER                 5                 35
  NEVER USED                  1                 39
[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
D66V38, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    6  2
  14Q LOSS WILD-TYPE 67 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      6    2
  14Q LOSS WILD-TYPE   67   12
         clus
vv        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ABSENT                 6                 67
  PRESENT                2                 12
[1] 2 2
[1] FALSE
D66V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  14Q LOSS MUTATED     0    0   1    6    3  2   0    1    0   0   0  0  1
  14Q LOSS WILD-TYPE   2    1  21   45   18  1   6    5    8  13   2  1  6
D66V40, multiclass
      clus
vv     14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 1                 21
  T1B1                6                 45
  T1B2                3                 18
  T2                  2                  1
  T2A                 0                  6
  T2A1                1                  5
  T2A2                0                  8
  T2B                 0                 13
  T3B                 0                  2
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V41, continuous

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    18   4
  15Q LOSS WILD-TYPE 119  28
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                147 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 28 
$`15Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-C5-A1M9 TCGA-C5-A1MH TCGA-C5-A2LV TCGA-C5-A7CG TCGA-C5-A7CH 
       57.04        35.01        38.99        73.45       182.93        25.35 
TCGA-C5-A7UC TCGA-DR-A0ZL TCGA-DS-A7WH TCGA-EA-A439 TCGA-EA-A556 TCGA-EK-A2GZ 
       17.19        87.75         7.33        14.50        14.89        12.59 
TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-IR-A3LH TCGA-LP-A4AX 
        1.18         0.10        21.67         4.11        78.71         0.07 
TCGA-MU-A8JM TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42         2.96         3.72         3.45 

$`15Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        23.67        11.44        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-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS 
       35.61         0.46         2.43        40.93         3.58        44.22 
TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       73.18        83.05        78.35       100.14        38.43         0.82 
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-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
       15.48         9.67        73.41        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        9.34        13.61         2.73        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WI 
      117.99       118.65        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 
        0.76        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B 
       13.05         1.18        14.50         1.35         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.66        12.82         0.26         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.99        14.96        13.58        13.48        45.96         6.64 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.53         0.59         0.07         4.04         0.03         0.36 
TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN 
       23.70         2.24         0.07         0.10         0.10         0.03 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
       20.35         7.92         6.94        14.70         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17         0.66         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.45         1.58         1.48         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 
        1.32         1.97         1.12        25.41        20.78        14.93 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI 
      147.39       137.16        66.81       117.40        96.95        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36        14.43        16.64        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 
       15.58        10.06         5.13         0.10         0.89         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R3 
       13.87         0.03        29.72         0.07         4.34         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            182.93             177.04 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            14.695             13.480 
[1] "0.1 - 182.9 (14.7)" "0.0 - 177.0 (13.5)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 T1 T2+T3+T4
  15Q LOSS MUTATED   13        6
  15Q LOSS WILD-TYPE 84       33
D67V3, multiclass
          clus
vv         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                     13                 84
  T2+T3+T4                6                 33
[1] 2 2
[1] FALSE
D67V4, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   15  4
  15Q LOSS WILD-TYPE 72 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     15    4
  15Q LOSS WILD-TYPE   72   36
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               15                 72
  1                4                 36
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED    9  1 10
  15Q LOSS WILD-TYPE 63  2 55
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                9                 63
  M1                1                  2
  MX               10                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED               1                               19
  15Q LOSS WILD-TYPE             1                              125
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  15Q LOSS MUTATED                                               0
  15Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  15Q LOSS MUTATED                                     2
  15Q LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  15Q LOSS MUTATED                                           1
  15Q LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  15Q LOSS MUTATED                                              1
  15Q LOSS WILD-TYPE                                            3
D67V6, multiclass
                                               clus
vv                                              15Q LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            19
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              15Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  1
  CERVICAL SQUAMOUS CELL CARCINOMA                             125
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3  21
  15Q LOSS WILD-TYPE  24 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3   21
  15Q LOSS WILD-TYPE   24  128
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 3                 24
  YES               21                128
[1] 2 2
[1] FALSE
D67V8, continuous
D67V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     3
  15Q LOSS WILD-TYPE                                7    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED                           6
  15Q LOSS WILD-TYPE                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           0    15
  15Q LOSS WILD-TYPE                                         1   115
D67V10, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    3                 12
  BLACK OR AFRICAN AMERICAN                                6                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                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"
D67V11, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     0  20
  15Q LOSS WILD-TYPE  11 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   20
  15Q LOSS WILD-TYPE   11  107
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               20                107
[1] 2 2
[1] FALSE
D67V12, continuous
D67V13, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    6  3
  15Q LOSS WILD-TYPE 42 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6    3
  15Q LOSS WILD-TYPE   42   16
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  TUMOR FREE                6                 42
  WITH TUMOR                3                 16
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  15Q LOSS MUTATED         1      1       0            20       2
  15Q LOSS WILD-TYPE       0      9       6           127      10
D67V14, multiclass
               clus
vv              15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES               20                127
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  15Q LOSS MUTATED    0  7 16  1  0
  15Q LOSS WILD-TYPE 14 76 56  0  5
D67V15, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  G1                0                 14
  G2                7                 76
  G3               16                 56
  G4                1                  0
  GX                0                  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"
D67V16, continuous
D67V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  15Q LOSS MUTATED                                             2
  15Q LOSS WILD-TYPE                                          19
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  15Q LOSS MUTATED                                        1
  15Q LOSS WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  15Q LOSS MUTATED                                                 0
  15Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  15Q LOSS MUTATED                4                   9
  15Q LOSS WILD-TYPE             32                  74
D67V18, multiclass
                                                 clus
vv                                                15Q 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                                                 4
  LIFELONG NON-SMOKER                                            9
                                                 clus
vv                                                15Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  32
  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"
D67V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  15Q LOSS MUTATED             1        5             2        0
  15Q LOSS WILD-TYPE          16       32             9        5
D67V20, multiclass
               clus
vv              15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COMBINATION                  1                 16
  EXTERNAL                     5                 32
  EXTERNAL BEAM                2                  9
  INTERNAL                     0                  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"
D67V21, binary
                    cls
clus                 0 1
  15Q LOSS MUTATED   2 0
  15Q LOSS WILD-TYPE 9 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    0
  15Q LOSS WILD-TYPE    9    3
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CGY                2                  9
  GY                 0                  3
[1] 2 2
[1] FALSE
D67V22, continuous
D67V23, continuous
D67V24, continuous
D67V25, continuous
D67V26, continuous
D67V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  15Q LOSS MUTATED                                     0
  15Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  15Q LOSS MUTATED                                     1
  15Q LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  15Q LOSS MUTATED                         1                       0
  15Q LOSS WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  15Q LOSS MUTATED                         1
  15Q LOSS WILD-TYPE                       4
D67V28, multiclass
                                     clus
vv                                    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            1                  8
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  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)
  15Q LOSS MUTATED                                               0
  15Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  15Q LOSS MUTATED                                                1
  15Q LOSS WILD-TYPE                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  15Q LOSS MUTATED                                                                                   7
  15Q LOSS WILD-TYPE                                                                                47
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  15Q LOSS MUTATED                                                                                             11
  15Q LOSS WILD-TYPE                                                                                           66
D67V29, multiclass
                                                                                              clus
vv                                                                                             15Q 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)                           7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               11
                                                                                              clus
vv                                                                                             15Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                9
  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)                 66
[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"
D67V30, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    6  6
  15Q LOSS WILD-TYPE 48 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6    6
  15Q LOSS WILD-TYPE   48   53
         clus
vv        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ABSENT                 6                 48
  PRESENT                6                 53
[1] 2 2
[1] FALSE
D67V31, continuous
D67V32, continuous
D67V33, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    5 14
  15Q LOSS WILD-TYPE 30 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5   14
  15Q LOSS WILD-TYPE   30   67
                                          clus
vv                                         15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    5                 30
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               14                 67
[1] 2 2
[1] FALSE
D67V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  15Q LOSS MUTATED       0                   17                   1
  15Q LOSS WILD-TYPE     3                   96                   4
D67V35, multiclass
                      clus
vv                     15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               17                 96
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  15Q LOSS MUTATED              1           7          4
  15Q LOSS WILD-TYPE            7          33         36
D67V36, multiclass
              clus
vv             15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 7                 33
  NEVER USED                  4                 36
[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
D67V38, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    6  1
  15Q LOSS WILD-TYPE 67 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6    1
  15Q LOSS WILD-TYPE   67   13
         clus
vv        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ABSENT                 6                 67
  PRESENT                1                 13
[1] 2 2
[1] FALSE
D67V39, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                  7 
        TCGA-C5-A1BN         TCGA-C5-A1MN         TCGA-C5-A1MP 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y 
"15Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  15Q LOSS MUTATED     0    0   4    8    1  0   1    2    0   2   1  0  1
  15Q LOSS WILD-TYPE   2    1  18   43   20  3   5    4    8  11   1  1  6
D67V40, multiclass
      clus
vv     15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 4                 18
  T1B1                8                 43
  T1B2                1                 20
  T2                  0                  3
  T2A                 1                  5
  T2A1                2                  4
  T2A2                0                  8
  T2B                 2                 11
  T3B                 1                  1
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V41, continuous

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    13   4
  16P LOSS WILD-TYPE 124  28
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                17                152 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 28 
$`16P LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LT TCGA-C5-A3HE 
       23.67       173.29        35.01        57.73        73.18        18.02 
TCGA-C5-A7CG TCGA-C5-A7UC TCGA-C5-A7X5 TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2RJ 
      182.93        17.19        13.61         1.81         0.53         1.18 
TCGA-EK-A2RM TCGA-FU-A3TX TCGA-HM-A6W2 TCGA-IR-A3LB TCGA-IR-A3LF 
        2.24         1.48         4.11        66.81        96.95 

$`16P LOSS 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-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       31.40        46.32        30.21        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LV 
        0.46         2.43        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         0.82        52.01 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL 
       17.85        20.42        25.35       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 
        9.67        73.41        85.55        60.69        94.95         9.34 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
        2.73        87.75        58.88        36.76         2.66       117.99 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      118.65        22.98        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        0.76        12.36         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 
       13.05         1.18        14.50         1.35         1.35        14.50 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         0.26        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
        0.69        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       45.96         6.64         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.36        23.70         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.12         1.22        23.84         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J 
        1.02         1.45         1.58         0.82         3.52         1.35 
TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.32         1.97         1.12        25.41        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       117.40        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK 
       26.56        36.36        14.43        16.64        19.33        20.48 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       15.58        10.06         5.13         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT 
        4.34         2.96         3.72         3.45         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 
        3.72         5.75         4.80         6.25        19.59         3.88 
TCGA-UC-A7PD TCGA-UC-A7PF 
       11.67        93.99 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.53               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            182.93             177.04 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            18.020             12.935 
[1] "0.5 - 182.9 (18.0)" "0.0 - 177.0 (12.9)"
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 T1 T2+T3+T4
  16P LOSS MUTATED   13        2
  16P LOSS WILD-TYPE 84       37
D68V3, multiclass
          clus
vv         16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                     13                 84
  T2+T3+T4                2                 37
[1] 2 2
[1] FALSE
D68V4, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   13  2
  16P LOSS WILD-TYPE 74 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     13    2
  16P LOSS WILD-TYPE   74   38
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               13                 74
  1                2                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED   12  1  2
  16P LOSS WILD-TYPE 60  2 63
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               12                 60
  M1                1                  2
  MX                2                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED               1                               15
  16P LOSS WILD-TYPE             1                              129
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16P LOSS MUTATED                                               1
  16P LOSS WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16P LOSS MUTATED                                     3
  16P LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16P LOSS MUTATED                                           0
  16P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16P LOSS MUTATED                                              0
  16P LOSS WILD-TYPE                                            4
D68V6, multiclass
                                               clus
vv                                              16P LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            15
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              16P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  1
  CERVICAL SQUAMOUS CELL CARCINOMA                             129
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D68V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  17
  16P LOSS WILD-TYPE  24 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   17
  16P LOSS WILD-TYPE   24  132
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 3                 24
  YES               17                132
[1] 2 2
[1] FALSE
D68V8, continuous
D68V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     1
  16P LOSS WILD-TYPE                                7    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED                           3
  16P LOSS WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           0    15
  16P LOSS WILD-TYPE                                         1   115
D68V10, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    1                 14
  BLACK OR AFRICAN AMERICAN                                3                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                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"
D68V11, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0  14
  16P LOSS WILD-TYPE  11 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   14
  16P LOSS WILD-TYPE   11  113
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO               14                113
[1] 2 2
[1] FALSE
D68V12, continuous
D68V13, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    4  1
  16P LOSS WILD-TYPE 44 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    1
  16P LOSS WILD-TYPE   44   18
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  TUMOR FREE                4                 44
  WITH TUMOR                1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  16P LOSS MUTATED         0      0       1            18       1
  16P LOSS WILD-TYPE       1     10       5           129      11
D68V14, multiclass
               clus
vv              16P LOSS MUTATED 16P LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      1                  5
  UNITED STATES               18                129
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  16P LOSS MUTATED    1  6 13  0  0
  16P LOSS WILD-TYPE 13 77 59  1  5
D68V15, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  G1                1                 13
  G2                6                 77
  G3               13                 59
  G4                0                  1
  GX                0                  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"
D68V16, continuous
D68V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16P LOSS MUTATED                                             3
  16P LOSS WILD-TYPE                                          18
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  16P LOSS MUTATED                                        1
  16P LOSS WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  16P LOSS MUTATED                                                 0
  16P LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16P LOSS MUTATED                2                   6
  16P LOSS WILD-TYPE             34                  77
D68V18, multiclass
                                                 clus
vv                                                16P 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                                                 2
  LIFELONG NON-SMOKER                                            6
                                                 clus
vv                                                16P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  34
  LIFELONG NON-SMOKER                                             77
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  16P LOSS MUTATED             1        5             2        0
  16P LOSS WILD-TYPE          16       32             9        5
D68V20, multiclass
               clus
vv              16P LOSS MUTATED 16P LOSS WILD-TYPE
  COMBINATION                  1                 16
  EXTERNAL                     5                 32
  EXTERNAL BEAM                2                  9
  INTERNAL                     0                  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"
D68V21, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  0
  16P LOSS WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    0
  16P LOSS WILD-TYPE   10    3
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D68V22, continuous
D68V23, continuous
D68V24, continuous
D68V25, continuous
D68V26, continuous
D68V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  16P LOSS MUTATED                                     0
  16P LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  16P LOSS MUTATED                                     1
  16P LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  16P LOSS MUTATED                         0                       0
  16P LOSS WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16P LOSS MUTATED                         0
  16P LOSS WILD-TYPE                       5
D68V28, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 22 
        TCGA-C5-A0TN         TCGA-C5-A1BE         TCGA-C5-A1BM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-DR-A0ZM         TCGA-DS-A0VK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-EA-A50E         TCGA-EK-A2RN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-EX-A1H5         TCGA-EX-A449 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-HM-A4S6         TCGA-IR-A3LH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-MU-A8JM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UC-A7PD 
"16P LOSS WILD-TYPE" 
                    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                                                0
  16P LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16P LOSS MUTATED                                                                                   5
  16P LOSS WILD-TYPE                                                                                49
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16P LOSS MUTATED                                                                                              6
  16P LOSS WILD-TYPE                                                                                           71
D68V29, multiclass
                                                                                              clus
vv                                                                                             16P 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)                           5
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                6
                                                                                              clus
vv                                                                                             16P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            49
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 71
[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"
D68V30, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    4  7
  16P LOSS WILD-TYPE 50 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    7
  16P LOSS WILD-TYPE   50   52
         clus
vv        16P LOSS MUTATED 16P LOSS WILD-TYPE
  ABSENT                 4                 50
  PRESENT                7                 52
[1] 2 2
[1] FALSE
D68V31, continuous
D68V32, continuous
D68V33, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    6  5
  16P LOSS WILD-TYPE 29 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      6    5
  16P LOSS WILD-TYPE   29   76
                                          clus
vv                                         16P LOSS MUTATED 16P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                5                 76
[1] 2 2
[1] FALSE
D68V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  16P LOSS MUTATED       1                   13                   1
  16P LOSS WILD-TYPE     2                  100                   4
D68V35, multiclass
                      clus
vv                     16P LOSS MUTATED 16P LOSS WILD-TYPE
  OTHER                               1                  2
  RADICAL HYSTERECTOMY               13                100
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16P LOSS MUTATED              1           3          5
  16P LOSS WILD-TYPE            7          37         35
D68V36, multiclass
              clus
vv             16P LOSS MUTATED 16P LOSS WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 3                 37
  NEVER USED                  5                 35
[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, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    6  1
  16P LOSS WILD-TYPE 67 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      6    1
  16P LOSS WILD-TYPE   67   13
         clus
vv        16P LOSS MUTATED 16P LOSS WILD-TYPE
  ABSENT                 6                 67
  PRESENT                1                 13
[1] 2 2
[1] FALSE
D68V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  16P LOSS MUTATED     0    0   5    5    3  0   1    0    0   0   1  0  0
  16P LOSS WILD-TYPE   2    1  17   46   18  3   5    6    8  13   1  1  7
D68V40, multiclass
      clus
vv     16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 5                 17
  T1B1                5                 46
  T1B2                3                 18
  T2                  0                  3
  T2A                 1                  5
  T2A1                0                  6
  T2A2                0                  8
  T2B                 0                 13
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V41, continuous

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    20   2
  16Q LOSS WILD-TYPE 117  30
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                147 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 30 
$`16Q LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BL TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A2LS TCGA-C5-A2LT 
       23.67       173.29        35.01        57.73        44.22        73.18 
TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A3HE TCGA-C5-A7CG TCGA-C5-A7CO TCGA-DS-A7WH 
       83.05        38.43        18.02       182.93        73.41         7.33 
TCGA-EA-A43B TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EX-A1H6 TCGA-FU-A3TX TCGA-FU-A770 
        1.81         0.53         1.18         7.92         1.48         1.12 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-MY-A5BF 
      137.16        66.81        96.95         4.34 

$`16Q LOSS 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-A1M7 TCGA-C5-A1M8 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       31.40        46.32        30.21        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LV TCGA-C5-A2LY 
        0.46         2.43        40.93         3.58        73.45        78.35 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CH 
      100.14         0.82        52.01        17.85        20.42        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UC TCGA-C5-A7UE 
      101.82       134.33        15.48         9.67        17.19        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL 
       60.69        94.95         9.34        13.61         2.73        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       58.88        36.76         2.66       117.99       118.65        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         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35         1.35        14.50        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 
       13.58        13.48        12.59        45.96         6.64         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         4.04         0.03         0.36        23.70         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70         4.47         6.12         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-HG-A2PA 
        0.82         3.52         1.35         1.32         1.97        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LC 
       21.67        20.78        14.93         4.11       147.39       117.40 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI 
       78.71        81.96        26.56        36.36        14.43        16.64 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU 
       19.33        20.48        15.58        10.06         5.13         0.10 
TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.89         0.07         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
       29.72         0.07         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.53               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            182.93             177.04 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             36.72              12.82 
[1] "0.5 - 182.9 (36.7)" "0.0 - 177.0 (12.8)"
[1] "hr=" "4.3"
D69V2, continuous
                    vv
clus                 T1 T2+T3+T4
  16Q LOSS MUTATED   17        4
  16Q LOSS WILD-TYPE 80       35
D69V3, multiclass
          clus
vv         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                     17                 80
  T2+T3+T4                4                 35
[1] 2 2
[1] FALSE
D69V4, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   17  4
  16Q LOSS WILD-TYPE 70 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     17    4
  16Q LOSS WILD-TYPE   70   36
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               17                 70
  1                4                 36
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16Q LOSS MUTATED   13  0  8
  16Q LOSS WILD-TYPE 59  3 57
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               13                 59
  M1                0                  3
  MX                8                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED               0                               15
  16Q LOSS WILD-TYPE             2                              129
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  16Q LOSS MUTATED                                               3
  16Q LOSS WILD-TYPE                                             1
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  16Q LOSS MUTATED                                     7
  16Q LOSS WILD-TYPE                                  13
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  16Q LOSS MUTATED                                           1
  16Q LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  16Q LOSS MUTATED                                              0
  16Q LOSS WILD-TYPE                                            4
D69V6, multiclass
                                               clus
vv                                              16Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            15
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              16Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             129
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     4  22
  16Q LOSS WILD-TYPE  23 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4   22
  16Q LOSS WILD-TYPE   23  127
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 4                 23
  YES               22                127
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     1
  16Q LOSS WILD-TYPE                                7    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED                           1
  16Q LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           0    23
  16Q LOSS WILD-TYPE                                         1   107
D69V10, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    1                 14
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   23                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"
D69V11, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  18
  16Q LOSS WILD-TYPE  10 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   18
  16Q LOSS WILD-TYPE   10  109
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               18                109
[1] 2 2
[1] FALSE
D69V12, continuous
D69V13, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    7  1
  16Q LOSS WILD-TYPE 41 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    1
  16Q LOSS WILD-TYPE   41   18
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  TUMOR FREE                7                 41
  WITH TUMOR                1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  16Q LOSS MUTATED         0      0       1            24       1
  16Q LOSS WILD-TYPE       1     10       5           123      11
D69V14, multiclass
               clus
vv              16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      1                  5
  UNITED STATES               24                123
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  16Q LOSS MUTATED    4 12 10  0  0
  16Q LOSS WILD-TYPE 10 71 62  1  5
D69V15, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  G1                4                 10
  G2               12                 71
  G3               10                 62
  G4                0                  1
  GX                0                  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"
D69V16, continuous
D69V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  16Q LOSS MUTATED                                             3
  16Q LOSS WILD-TYPE                                          18
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  16Q LOSS MUTATED                                        2
  16Q LOSS WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  16Q LOSS MUTATED                                                 0
  16Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  16Q LOSS MUTATED                4                  12
  16Q LOSS WILD-TYPE             32                  71
D69V18, multiclass
                                                 clus
vv                                                16Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    3
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                           12
                                                 clus
vv                                                16Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  32
  LIFELONG NON-SMOKER                                             71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  16Q LOSS MUTATED             2        5             2        1
  16Q LOSS WILD-TYPE          15       32             9        4
D69V20, multiclass
               clus
vv              16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COMBINATION                  2                 15
  EXTERNAL                     5                 32
  EXTERNAL BEAM                2                  9
  INTERNAL                     1                  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"
D69V21, binary
                    cls
clus                 0 1
  16Q LOSS MUTATED   2 0
  16Q LOSS WILD-TYPE 9 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    0
  16Q LOSS WILD-TYPE    9    3
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CGY                2                  9
  GY                 0                  3
[1] 2 2
[1] FALSE
D69V22, continuous
D69V23, continuous
D69V24, continuous
D69V25, continuous
D69V26, continuous
D69V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  16Q LOSS MUTATED                                     0
  16Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  16Q LOSS MUTATED                                     1
  16Q LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  16Q LOSS MUTATED                         0                       0
  16Q LOSS WILD-TYPE                       9                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  16Q LOSS MUTATED                         1
  16Q LOSS WILD-TYPE                       4
D69V28, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 21 
        TCGA-C5-A0TN         TCGA-C5-A1BE         TCGA-C5-A1BM 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EK-A2RN         TCGA-EK-A2RO 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A8JM         TCGA-UC-A7PD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
                    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                                                0
  16Q LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  16Q LOSS MUTATED                                                                                  10
  16Q LOSS WILD-TYPE                                                                                44
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  16Q LOSS MUTATED                                                                                              9
  16Q LOSS WILD-TYPE                                                                                           68
D69V29, multiclass
                                                                                              clus
vv                                                                                             16Q 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)                          10
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                9
                                                                                              clus
vv                                                                                             16Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  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)                 68
[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"
D69V30, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    8  8
  16Q LOSS WILD-TYPE 46 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8    8
  16Q LOSS WILD-TYPE   46   51
         clus
vv        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ABSENT                 8                 46
  PRESENT                8                 51
[1] 2 2
[1] FALSE
D69V31, continuous
D69V32, continuous
D69V33, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    6  6
  16Q LOSS WILD-TYPE 29 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      6    6
  16Q LOSS WILD-TYPE   29   75
                                          clus
vv                                         16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                6                 75
[1] 2 2
[1] FALSE
D69V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  16Q LOSS MUTATED       2                   15                   2
  16Q LOSS WILD-TYPE     1                   98                   3
D69V35, multiclass
                      clus
vv                     16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  OTHER                               2                  1
  RADICAL HYSTERECTOMY               15                 98
  SIMPLE HYSTERECTOMY                 2                  3
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  16Q LOSS MUTATED              2           6          6
  16Q LOSS WILD-TYPE            6          34         34
D69V36, multiclass
              clus
vv             16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CURRENT USER                2                  6
  FORMER USER                 6                 34
  NEVER USED                  6                 34
[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
D69V38, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   12  1
  16Q LOSS WILD-TYPE 61 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     12    1
  16Q LOSS WILD-TYPE   61   13
         clus
vv        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ABSENT                12                 61
  PRESENT                1                 13
[1] 2 2
[1] FALSE
D69V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  16Q LOSS MUTATED     0    0   4    9    4  1   0    0    2   0   1  0  0
  16Q LOSS WILD-TYPE   2    1  18   42   17  2   6    6    6  13   1  1  7
D69V40, multiclass
      clus
vv     16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 4                 18
  T1B1                9                 42
  T1B2                4                 17
  T2                  1                  2
  T2A                 0                  6
  T2A1                0                  6
  T2A2                2                  6
  T2B                 0                 13
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V41, continuous

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    37  13
  17P LOSS WILD-TYPE 100  19
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                50                119 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                 19 
$`17P LOSS MUTATED`
TCGA-C5-A1BE TCGA-C5-A1BJ TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 
       68.84       144.16       173.29         5.46        19.86        67.46 
TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A2M1 TCGA-C5-A7CL 
       38.99        40.93        73.18        83.05        38.43        15.48 
TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL 
       73.41        17.19         9.34        13.61         2.73        87.75 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A439 TCGA-EA-A44S 
       36.76         2.66       118.65        12.36        14.50        12.66 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2PG 
       14.99        14.96        13.58        13.48        45.96         0.53 
TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A3GJ TCGA-EX-A1H5 
        0.03         1.18         2.24         0.10         0.10        20.35 
TCGA-EX-A3L1 TCGA-EX-A69M TCGA-FU-A3NI TCGA-IR-A3LH TCGA-IR-A3LK TCGA-JW-A5VI 
        6.94         6.12         1.45        78.71        26.56        16.64 
TCGA-JW-A69B TCGA-LP-A4AU TCGA-LP-A4AW TCGA-MU-A5YI TCGA-PN-A8MA TCGA-Q1-A5R2 
       10.06         0.10         0.89         0.03         2.96         3.45 
TCGA-Q1-A6DT TCGA-RA-A741 
        3.39         3.88 

$`17P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BF TCGA-C5-A1BI 
       49.48        57.04        23.67        11.44        18.74        36.56 
TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1M6 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 
      177.04        82.85        31.40        46.32        30.21        35.01 
TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP 
       57.73        53.16        35.61         0.46         2.43         3.58 
TCGA-C5-A2LS TCGA-C5-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD 
       44.22        73.45        78.35       100.14         0.82        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       182.93        25.35       101.82 
TCGA-C5-A7CK TCGA-C5-A7CM TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-DR-A0ZM 
      134.33         9.67        85.55        60.69        94.95        58.88 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99        22.98        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD 
        0.76         1.74         1.32         0.82         0.62        13.05 
TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A43B TCGA-EA-A4BA 
        1.18        14.50         1.35         1.35         1.81        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EK-A2GZ 
        0.26        14.89         1.48        13.91         0.69        12.59 
TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL 
        6.64         0.59         0.07         4.04         0.36        23.70 
TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L 
        0.07         0.10         0.03         7.92        14.70         4.47 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22        23.84         0.92         2.17         0.66         1.02 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LI TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       81.96        36.36        14.43        19.33        20.48        15.58 
TCGA-JW-A852 TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A8JM TCGA-MY-A5BD 
        5.13         0.07         0.82        13.87         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        0.07         4.34         3.72         5.85         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59        11.67        93.99 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            173.29             182.93 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            13.595             13.050 
[1] "0.0 - 173.3 (13.6)" "0.0 - 182.9 (13.1)"
[1] "hr=" "1.6"
D70V2, continuous
                    vv
clus                 T1 T2+T3+T4
  17P LOSS MUTATED   25       11
  17P LOSS WILD-TYPE 72       28
D70V3, multiclass
          clus
vv         17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                     25                 72
  T2+T3+T4               11                 28
[1] 2 2
[1] FALSE
D70V4, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   20 11
  17P LOSS WILD-TYPE 67 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     20   11
  17P LOSS WILD-TYPE   67   29
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               20                 67
  1               11                 29
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED   23  0 14
  17P LOSS WILD-TYPE 49  3 51
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               23                 49
  M1                0                  3
  MX               14                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED               0                               48
  17P LOSS WILD-TYPE             2                               96
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17P LOSS MUTATED                                               0
  17P LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17P LOSS MUTATED                                     3
  17P LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17P LOSS MUTATED                                           0
  17P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17P LOSS MUTATED                                              1
  17P LOSS WILD-TYPE                                            3
D70V6, multiclass
                                               clus
vv                                              17P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            48
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              17P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                              96
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    10  42
  17P LOSS WILD-TYPE  17 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     10   42
  17P LOSS WILD-TYPE   17  107
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                10                 17
  YES               42                107
[1] 2 2
[1] FALSE
D70V8, continuous
D70V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  2     8
  17P LOSS WILD-TYPE                                5     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED                           6
  17P LOSS WILD-TYPE                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           1    35
  17P LOSS WILD-TYPE                                         0    95
D70V10, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  5
  ASIAN                                                    8                  7
  BLACK OR AFRICAN AMERICAN                                6                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   35                 95
[1] 5 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
  17P LOSS MUTATED    3 37
  17P LOSS WILD-TYPE  8 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3   37
  17P LOSS WILD-TYPE    8   90
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               37                 90
[1] 2 2
[1] FALSE
D70V12, continuous
D70V13, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   17  6
  17P LOSS WILD-TYPE 31 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     17    6
  17P LOSS WILD-TYPE   31   13
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  TUMOR FREE               17                 31
  WITH TUMOR                6                 13
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  17P LOSS MUTATED         1      1       1            42       7
  17P LOSS WILD-TYPE       0      9       5           105       5
D70V14, multiclass
               clus
vv              17P LOSS MUTATED 17P LOSS WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       1                  9
  UKRAINE                      1                  5
  UNITED STATES               42                105
  VIETNAM                      7                  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                 G1 G2 G3 G4 GX
  17P LOSS MUTATED    1 23 24  1  3
  17P LOSS WILD-TYPE 13 60 48  0  2
D70V15, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  G1                1                 13
  G2               23                 60
  G3               24                 48
  G4                1                  0
  GX                3                  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"
D70V16, continuous
D70V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17P LOSS MUTATED                                             7
  17P LOSS WILD-TYPE                                          14
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  17P LOSS MUTATED                                        4
  17P LOSS WILD-TYPE                                      4
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  17P LOSS MUTATED                                                 0
  17P LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17P LOSS MUTATED                9                  21
  17P LOSS WILD-TYPE             27                  62
D70V18, multiclass
                                                 clus
vv                                                17P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    7
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 9
  LIFELONG NON-SMOKER                                           21
                                                 clus
vv                                                17P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     14
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           4
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  27
  LIFELONG NON-SMOKER                                             62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  17P LOSS MUTATED             8       11             3        3
  17P LOSS WILD-TYPE           9       26             8        2
D70V20, multiclass
               clus
vv              17P LOSS MUTATED 17P LOSS WILD-TYPE
  COMBINATION                  8                  9
  EXTERNAL                    11                 26
  EXTERNAL BEAM                3                  8
  INTERNAL                     3                  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"
D70V21, binary
                    cls
clus                 0 1
  17P LOSS MUTATED   3 2
  17P LOSS WILD-TYPE 8 1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3    2
  17P LOSS WILD-TYPE    8    1
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  CGY                3                  8
  GY                 2                  1
[1] 2 2
[1] FALSE
D70V22, continuous
D70V23, continuous
D70V24, continuous
D70V25, continuous
D70V26, continuous
D70V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  17P LOSS MUTATED                                     0
  17P LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  17P LOSS MUTATED                                     2
  17P LOSS WILD-TYPE                                   4
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  17P LOSS MUTATED                         4                       0
  17P LOSS WILD-TYPE                       5                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17P LOSS MUTATED                         3
  17P LOSS WILD-TYPE                       2
D70V28, multiclass
                                     clus
vv                                    17P LOSS MUTATED 17P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  4
  OTHER LOCATION, SPECIFY                            4                  5
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            3                  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)
  17P LOSS MUTATED                                               1
  17P LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  17P LOSS MUTATED                                                5
  17P LOSS WILD-TYPE                                              5
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17P LOSS MUTATED                                                                                  18
  17P LOSS WILD-TYPE                                                                                36
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17P LOSS MUTATED                                                                                             20
  17P LOSS WILD-TYPE                                                                                           57
D70V29, multiclass
                                                                                              clus
vv                                                                                             17P 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)                          18
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               20
                                                                                              clus
vv                                                                                             17P LOSS WILD-TYPE
  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)                            36
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 57
[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"
D70V30, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   14 17
  17P LOSS WILD-TYPE 40 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     14   17
  17P LOSS WILD-TYPE   40   42
         clus
vv        17P LOSS MUTATED 17P LOSS WILD-TYPE
  ABSENT                14                 40
  PRESENT               17                 42
[1] 2 2
[1] FALSE
D70V31, continuous
D70V32, continuous
D70V33, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   14 27
  17P LOSS WILD-TYPE 21 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     14   27
  17P LOSS WILD-TYPE   21   54
                                          clus
vv                                         17P LOSS MUTATED 17P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                   14                 21
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               27                 54
[1] 2 2
[1] FALSE
D70V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  17P LOSS MUTATED       0                   30                   1
  17P LOSS WILD-TYPE     3                   83                   4
D70V35, multiclass
                      clus
vv                     17P LOSS MUTATED 17P LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               30                 83
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17P LOSS MUTATED              2          10         12
  17P LOSS WILD-TYPE            6          30         28
D70V36, multiclass
              clus
vv             17P LOSS MUTATED 17P LOSS WILD-TYPE
  CURRENT USER                2                  6
  FORMER USER                10                 30
  NEVER USED                 12                 28
[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
D70V38, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   21  2
  17P LOSS WILD-TYPE 52 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     21    2
  17P LOSS WILD-TYPE   52   12
         clus
vv        17P LOSS MUTATED 17P LOSS WILD-TYPE
  ABSENT                21                 52
  PRESENT                2                 12
[1] 2 2
[1] FALSE
D70V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  17P LOSS MUTATED     1    1   6   12    5  2   1    3    1   4   0  0  2
  17P LOSS WILD-TYPE   1    0  16   39   16  1   5    3    7   9   2  1  5
D70V40, multiclass
      clus
vv     17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1A                 1                  1
  T1A1                1                  0
  T1B                 6                 16
  T1B1               12                 39
  T1B2                5                 16
  T2                  2                  1
  T2A                 1                  5
  T2A1                3                  3
  T2A2                1                  7
  T2B                 4                  9
  T3B                 0                  2
  T4                  0                  1
  TX                  2                  5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V41, continuous

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    11   5
  17Q LOSS WILD-TYPE 126  27
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                16                153 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 27 
$`17Q LOSS MUTATED`
TCGA-C5-A1MH TCGA-C5-A1MN TCGA-C5-A2LT TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UH 
       38.99        40.93        73.18        73.41        17.19        60.69 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EK-A2PG 
        9.34         2.73        36.76       118.65        12.36         0.53 
TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RN TCGA-JW-A5VI 
        0.03         1.18         0.10        16.64 

$`17Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MP 
       57.73        53.16        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 
        0.82        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7UE 
       25.35       101.82       134.33        15.48         9.67        85.55 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
       94.95        13.61        87.75        58.88         2.66       117.99 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S 
       14.50         1.35         1.35        14.50         1.81        12.66 
TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD 
       12.82         0.26        14.89         1.48        13.91         0.69 
TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 
       14.99        14.96        13.58        13.48        12.59        45.96 
TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RE TCGA-EK-A2RL 
        6.64         0.59         0.07         4.04         0.36        23.70 
TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.24         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70         4.47         6.12         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
       23.84         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF 
        4.11       147.39       137.16        66.81       117.40        96.95 
TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ 
       78.71        81.96        26.56        36.36        14.43        19.33 
TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW 
       20.48        15.58        10.06         5.13         0.10         0.89 
TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD 
        0.07         0.82        13.87         0.03         5.42        29.72 
TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 
        0.07         4.34         2.96         3.72         3.45         5.85 
TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V 
        3.39         3.72         5.75         4.80         6.25        19.59 
TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        3.88        11.67        93.99 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.03               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            118.65             182.93 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            16.915             13.480 
[1] "0.0 - 118.7 (16.9)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.5"
D71V2, continuous
                    vv
clus                 T1 T2+T3+T4
  17Q LOSS MUTATED    8        3
  17Q LOSS WILD-TYPE 89       36
D71V3, multiclass
          clus
vv         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                      8                 89
  T2+T3+T4                3                 36
[1] 2 2
[1] FALSE
D71V4, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    7  3
  17Q LOSS WILD-TYPE 80 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7    3
  17Q LOSS WILD-TYPE   80   37
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                7                 80
  1                3                 37
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17Q LOSS MUTATED    6  0  5
  17Q LOSS WILD-TYPE 66  3 60
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                6                 66
  M1                0                  3
  MX                5                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED               0                               16
  17Q LOSS WILD-TYPE             2                              128
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  17Q LOSS MUTATED                                               0
  17Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  17Q LOSS MUTATED                                     0
  17Q LOSS WILD-TYPE                                  20
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  17Q LOSS MUTATED                                           0
  17Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  17Q LOSS MUTATED                                              1
  17Q LOSS WILD-TYPE                                            3
D71V6, multiclass
                                               clus
vv                                              17Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            16
  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                                              17Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             128
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           20
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4  13
  17Q LOSS WILD-TYPE  23 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4   13
  17Q LOSS WILD-TYPE   23  136
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 4                 23
  YES               13                136
[1] 2 2
[1] FALSE
D71V8, continuous
D71V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  2     0
  17Q LOSS WILD-TYPE                                5    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED                           1
  17Q LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           0    14
  17Q LOSS WILD-TYPE                                         1   116
D71V10, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  5
  ASIAN                                                    0                 15
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                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"
D71V11, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  13
  17Q LOSS WILD-TYPE  10 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   13
  17Q LOSS WILD-TYPE   10  114
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               13                114
[1] 2 2
[1] FALSE
D71V12, continuous
D71V13, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  1
  17Q LOSS WILD-TYPE 44 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    1
  17Q LOSS WILD-TYPE   44   18
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  TUMOR FREE                4                 44
  WITH TUMOR                1                 18
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  17Q LOSS MUTATED         0      1       0            16       0
  17Q LOSS WILD-TYPE       1      9       6           131      12
D71V14, multiclass
               clus
vv              17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES               16                131
  VIETNAM                      0                 12
[1] 5 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                 G1 G2 G3 G4 GX
  17Q LOSS MUTATED    0  8  9  0  0
  17Q LOSS WILD-TYPE 14 75 63  1  5
D71V15, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  G1                0                 14
  G2                8                 75
  G3                9                 63
  G4                0                  1
  GX                0                  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"
D71V16, continuous
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 23 
        TCGA-BI-A0VR         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1ME         TCGA-C5-A1MF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A7CM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-EX-A69M         TCGA-FU-A2QG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-HM-A3JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-MU-A5YI         TCGA-MU-A8JM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D71V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  17Q LOSS MUTATED                                             1
  17Q LOSS WILD-TYPE                                          20
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  17Q LOSS MUTATED                                        2
  17Q LOSS WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  17Q LOSS MUTATED                                                 0
  17Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  17Q LOSS MUTATED                4                   4
  17Q LOSS WILD-TYPE             32                  79
D71V18, multiclass
                                                 clus
vv                                                17Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                            4
                                                 clus
vv                                                17Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  32
  LIFELONG NON-SMOKER                                             79
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  17Q LOSS MUTATED             2        3             3        2
  17Q LOSS WILD-TYPE          15       34             8        3
D71V20, multiclass
               clus
vv              17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COMBINATION                  2                 15
  EXTERNAL                     3                 34
  EXTERNAL BEAM                3                  8
  INTERNAL                     2                  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"
D71V21, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  0
  17Q LOSS WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    0
  17Q LOSS WILD-TYPE   10    3
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D71V22, continuous
D71V23, continuous
D71V24, continuous
D71V25, continuous
D71V26, continuous
D71V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  17Q LOSS MUTATED                                     0
  17Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  17Q LOSS MUTATED                                     0
  17Q LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  17Q LOSS MUTATED                         2                       0
  17Q LOSS WILD-TYPE                       7                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  17Q LOSS MUTATED                         1
  17Q LOSS WILD-TYPE                       4
D71V28, multiclass
                                     clus
vv                                    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            2                  7
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  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)
  17Q LOSS MUTATED                                               0
  17Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  17Q LOSS MUTATED                                                0
  17Q LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  17Q LOSS MUTATED                                                                                   7
  17Q LOSS WILD-TYPE                                                                                47
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  17Q LOSS MUTATED                                                                                              5
  17Q LOSS WILD-TYPE                                                                                           72
D71V29, multiclass
                                                                                              clus
vv                                                                                             17Q 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)                           7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                5
                                                                                              clus
vv                                                                                             17Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  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)                 72
[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"
D71V30, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    5  4
  17Q LOSS WILD-TYPE 49 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5    4
  17Q LOSS WILD-TYPE   49   55
         clus
vv        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ABSENT                 5                 49
  PRESENT                4                 55
[1] 2 2
[1] FALSE
D71V31, continuous
D71V32, continuous
D71V33, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    6  7
  17Q LOSS WILD-TYPE 29 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      6    7
  17Q LOSS WILD-TYPE   29   74
                                          clus
vv                                         17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                7                 74
[1] 2 2
[1] FALSE
D71V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  17Q LOSS MUTATED       0                   10                   0
  17Q LOSS WILD-TYPE     3                  103                   5
D71V35, multiclass
                      clus
vv                     17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               10                103
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  17Q LOSS MUTATED              1           4          3
  17Q LOSS WILD-TYPE            7          36         37
D71V36, multiclass
              clus
vv             17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 4                 36
  NEVER USED                  3                 37
[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, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  0
  17Q LOSS WILD-TYPE 69 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE   69   14
         clus
vv        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ABSENT                 4                 69
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D71V39, continuous
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                  7 
        TCGA-C5-A1BN         TCGA-C5-A1MP         TCGA-EK-A2RO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-MU-A51Y 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-MU-A8JM 
"17Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  17Q LOSS MUTATED     0    0   3    3    2  0   1    0    0   2   0  0  0
  17Q LOSS WILD-TYPE   2    1  19   48   19  3   5    6    8  11   2  1  7
D71V40, multiclass
      clus
vv     17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 3                 19
  T1B1                3                 48
  T1B2                2                 19
  T2                  0                  3
  T2A                 1                  5
  T2A1                0                  6
  T2A2                0                  8
  T2B                 2                 11
  T3B                 0                  2
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V41, continuous

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    24   7
  18P LOSS WILD-TYPE 113  25
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                31                138 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 25 
$`18P LOSS MUTATED`
TCGA-C5-A1BJ TCGA-C5-A1M6 TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MN TCGA-C5-A2LV 
      144.16        31.40        35.61         0.46        40.93        73.45 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A7CH TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DS-A0VN 
       78.35        38.43        25.35        13.61         2.73       118.65 
TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A43B TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG 
        0.76        12.36         1.81        12.59         6.64         0.53 
TCGA-EK-A2RM TCGA-EX-A1H6 TCGA-EX-A69L TCGA-FU-A3EO TCGA-FU-A770 TCGA-HM-A3JJ 
        2.24         7.92         4.47         2.17         1.12        21.67 
TCGA-JW-A5VI TCGA-JW-A69B TCGA-LP-A4AX TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A73P 
       16.64        10.06         0.07         3.72         3.45         4.80 
TCGA-UC-A7PD 
       11.67 

$`18P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        57.04        23.67        11.44        68.84        18.74 
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ 
       36.56       177.04       173.29        82.85         5.46        19.86 
TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF 
       67.46        46.32        30.21        35.01        57.73        53.16 
TCGA-C5-A1MH TCGA-C5-A1MK TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LX 
       38.99         2.43         3.58        44.22        73.18        83.05 
TCGA-C5-A2LZ TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL 
      100.14         0.82        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 
      182.93       101.82       134.33        15.48         9.67        73.41 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-DR-A0ZL 
       17.19        85.55        60.69        94.95         9.34        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       16.18         7.33         8.28         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO 
       14.50        12.66        12.82         0.26        14.89         1.48 
TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R 
       13.91         0.69        14.99        14.96        13.58        13.48 
TCGA-EK-A2H0 TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
       45.96         0.59         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        1.18        23.70         0.10         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M TCGA-FU-A23K 
        0.03        20.35         6.94        14.70         6.12         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
       23.84         0.92         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA 
       25.41        20.78        14.93         4.11       147.39       137.16 
TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK 
       66.81       117.40        96.95        78.71        81.96        26.56 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 
       36.36        14.43        19.33        20.48        15.58         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM 
        0.10         0.89         0.82        13.87         0.03         5.42 
TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DT 
       29.72         0.07         4.34         2.96         5.85         3.39 
TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        3.72         5.75         6.25        19.59         3.88        93.99 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            144.16             182.93 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            10.060             14.465 
[1] "0.1 - 144.2 (10.1)" "0.0 - 182.9 (14.5)"
[1] "hr=" "1.5"
D72V2, continuous
                    vv
clus                 T1 T2+T3+T4
  18P LOSS MUTATED   18        4
  18P LOSS WILD-TYPE 79       35
D72V3, multiclass
          clus
vv         18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                     18                 79
  T2+T3+T4                4                 35
[1] 2 2
[1] FALSE
D72V4, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   15  5
  18P LOSS WILD-TYPE 72 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     15    5
  18P LOSS WILD-TYPE   72   35
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               15                 72
  1                5                 35
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED   10  0 13
  18P LOSS WILD-TYPE 62  3 52
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               10                 62
  M1                0                  3
  MX               13                 52
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED               0                               23
  18P LOSS WILD-TYPE             2                              121
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18P LOSS MUTATED                                               1
  18P LOSS WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18P LOSS MUTATED                                     7
  18P LOSS WILD-TYPE                                  13
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18P LOSS MUTATED                                           0
  18P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18P LOSS MUTATED                                              2
  18P LOSS WILD-TYPE                                            2
D72V6, multiclass
                                               clus
vv                                              18P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            23
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          7
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              18P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             121
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           13
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   2
[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"
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     7  26
  18P LOSS WILD-TYPE  20 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      7   26
  18P LOSS WILD-TYPE   20  123
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 7                 20
  YES               26                123
[1] 2 2
[1] FALSE
D72V8, continuous
D72V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  2     2
  18P LOSS WILD-TYPE                                5    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED                           5
  18P LOSS WILD-TYPE                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           0    24
  18P LOSS WILD-TYPE                                         1   106
D72V10, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  5
  ASIAN                                                    2                 13
  BLACK OR AFRICAN AMERICAN                                5                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   24                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"
D72V11, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  23
  18P LOSS WILD-TYPE   8 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   23
  18P LOSS WILD-TYPE    8  104
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               23                104
[1] 2 2
[1] FALSE
D72V12, continuous
D72V13, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    8  3
  18P LOSS WILD-TYPE 40 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      8    3
  18P LOSS WILD-TYPE   40   16
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  TUMOR FREE                8                 40
  WITH TUMOR                3                 16
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  18P LOSS MUTATED         0      2       1            29       1
  18P LOSS WILD-TYPE       1      8       5           118      11
D72V14, multiclass
               clus
vv              18P LOSS MUTATED 18P LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       2                  8
  UKRAINE                      1                  5
  UNITED STATES               29                118
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  18P LOSS MUTATED    2 18 12  0  1
  18P LOSS WILD-TYPE 12 65 60  1  4
D72V15, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  G1                2                 12
  G2               18                 65
  G3               12                 60
  G4                0                  1
  GX                1                  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"
D72V16, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                 24 
        TCGA-BI-A0VR         TCGA-C5-A1BL         TCGA-C5-A1BQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A7CM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-DS-A3LQ         TCGA-EX-A69M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3TX         TCGA-FU-A3WB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-HM-A4S6         TCGA-IR-A3L7 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-MU-A5YI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D72V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18P LOSS MUTATED                                             1
  18P LOSS WILD-TYPE                                          20
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  18P LOSS MUTATED                                        0
  18P LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  18P LOSS MUTATED                                                 0
  18P LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18P LOSS MUTATED                8                  17
  18P LOSS WILD-TYPE             28                  66
D72V18, multiclass
                                                 clus
vv                                                18P 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                                                 8
  LIFELONG NON-SMOKER                                           17
                                                 clus
vv                                                18P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  28
  LIFELONG NON-SMOKER                                             66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  18P LOSS MUTATED             5        4             2        1
  18P LOSS WILD-TYPE          12       33             9        4
D72V20, multiclass
               clus
vv              18P LOSS MUTATED 18P LOSS WILD-TYPE
  COMBINATION                  5                 12
  EXTERNAL                     4                 33
  EXTERNAL BEAM                2                  9
  INTERNAL                     1                  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"
D72V21, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    1  0
  18P LOSS WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    0
  18P LOSS WILD-TYPE   10    3
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D72V22, continuous
D72V23, continuous
D72V24, continuous
D72V25, continuous
D72V26, continuous
D72V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  18P LOSS MUTATED                                     0
  18P LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  18P LOSS MUTATED                                     0
  18P LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  18P LOSS MUTATED                         2                       0
  18P LOSS WILD-TYPE                       7                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18P LOSS MUTATED                         1
  18P LOSS WILD-TYPE                       4
D72V28, multiclass
                                     clus
vv                                    18P LOSS MUTATED 18P LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            2                  7
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  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)
  18P LOSS MUTATED                                               0
  18P LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18P LOSS MUTATED                                                2
  18P LOSS WILD-TYPE                                              8
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18P LOSS MUTATED                                                                                   9
  18P LOSS WILD-TYPE                                                                                45
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18P LOSS MUTATED                                                                                             16
  18P LOSS WILD-TYPE                                                                                           61
D72V29, multiclass
                                                                                              clus
vv                                                                                             18P 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)                           9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               16
                                                                                              clus
vv                                                                                             18P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                8
  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)                 61
[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"
D72V30, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   12  6
  18P LOSS WILD-TYPE 42 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     12    6
  18P LOSS WILD-TYPE   42   53
         clus
vv        18P LOSS MUTATED 18P LOSS WILD-TYPE
  ABSENT                12                 42
  PRESENT                6                 53
[1] 2 2
[1] FALSE
D72V31, continuous
D72V32, continuous
D72V33, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    6 13
  18P LOSS WILD-TYPE 29 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6   13
  18P LOSS WILD-TYPE   29   68
                                          clus
vv                                         18P LOSS MUTATED 18P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               13                 68
[1] 2 2
[1] FALSE
D72V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  18P LOSS MUTATED       0                   18                   1
  18P LOSS WILD-TYPE     3                   95                   4
D72V35, multiclass
                      clus
vv                     18P LOSS MUTATED 18P LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               18                 95
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18P LOSS MUTATED              2          12          6
  18P LOSS WILD-TYPE            6          28         34
D72V36, multiclass
              clus
vv             18P LOSS MUTATED 18P LOSS WILD-TYPE
  CURRENT USER                2                  6
  FORMER USER                12                 28
  NEVER USED                  6                 34
[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, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   14  0
  18P LOSS WILD-TYPE 59 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     14    0
  18P LOSS WILD-TYPE   59   14
         clus
vv        18P LOSS MUTATED 18P LOSS WILD-TYPE
  ABSENT                14                 59
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D72V39, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  8 
        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-HM-A3JK         TCGA-JW-A852 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  18P LOSS MUTATED     0    0   4   12    2  0   1    0    1   2   0  0  1
  18P LOSS WILD-TYPE   2    1  18   39   19  3   5    6    7  11   2  1  6
D72V40, multiclass
      clus
vv     18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 4                 18
  T1B1               12                 39
  T1B2                2                 19
  T2                  0                  3
  T2A                 1                  5
  T2A1                0                  6
  T2A2                1                  7
  T2B                 2                 11
  T3B                 0                  2
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V41, continuous

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    32  10
  18Q LOSS WILD-TYPE 105  22
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                42                127 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                10                 22 
$`18Q LOSS MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MN 
       31.40        35.01        57.73        35.61         0.46        40.93 
TCGA-C5-A2LY TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A7CH TCGA-C5-A7UC TCGA-C5-A7X5 
       78.35        38.43         0.82        25.35        17.19        13.61 
TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A43B 
        2.73        87.75       118.65         0.76        12.36         1.81 
TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2RM 
       14.89        12.59        45.96         6.64         0.53         2.24 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A3EO TCGA-FU-A770 TCGA-HM-A3JJ TCGA-IR-A3LA 
        7.92         6.94         2.17         1.12        21.67       137.16 
TCGA-IR-A3LB TCGA-IR-A3LH TCGA-JW-A5VI TCGA-JW-A69B TCGA-LP-A4AW TCGA-LP-A4AX 
       66.81        78.71        16.64        10.06         0.89         0.07 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-Q1-A73P TCGA-RA-A741 TCGA-UC-A7PD 
        3.72         3.45         3.39         4.80         3.88        11.67 

$`18Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
        2.43         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LZ TCGA-C5-A3HD TCGA-C5-A3HE TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG 
      100.14        52.01        18.02        17.85        20.42       182.93 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UE 
      101.82       134.33        15.48         9.67        73.41        85.55 
TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       60.69        94.95         9.34        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99        22.98        16.83        16.18         7.33         8.28 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        1.74         1.32         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A44S TCGA-EA-A4BA 
       14.50         1.35         1.35        14.50        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
        0.26         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       13.58        13.48         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.36         1.18        23.70         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M 
        0.10         0.03        20.35        14.70         4.47         6.12 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22        23.84         0.92         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
        1.97        25.41        20.78        14.93         4.11       147.39 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
      117.40        96.95        81.96        26.56        36.36        14.43 
TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A5U3 
       19.33        20.48        15.58         5.13         0.10         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73R TCGA-R2-A69V 
        2.96         5.85         3.72         5.75         6.25        19.59 
TCGA-UC-A7PF 
       93.99 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            137.16             182.93 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            12.015             13.910 
[1] "0.1 - 137.2 (12.0)" "0.0 - 182.9 (13.9)"
[1] "hr=" "1.6"
D73V2, continuous
                    vv
clus                 T1 T2+T3+T4
  18Q LOSS MUTATED   23        7
  18Q LOSS WILD-TYPE 74       32
D73V3, multiclass
          clus
vv         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                     23                 74
  T2+T3+T4                7                 32
[1] 2 2
[1] FALSE
D73V4, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   23  5
  18Q LOSS WILD-TYPE 64 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     23    5
  18Q LOSS WILD-TYPE   64   35
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               23                 64
  1                5                 35
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED   19  0 13
  18Q LOSS WILD-TYPE 53  3 52
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               19                 53
  M1                0                  3
  MX               13                 52
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED               0                               29
  18Q LOSS WILD-TYPE             2                              115
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  18Q LOSS MUTATED                                               1
  18Q LOSS WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  18Q LOSS MUTATED                                    11
  18Q LOSS WILD-TYPE                                   9
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  18Q LOSS MUTATED                                           2
  18Q LOSS WILD-TYPE                                         0
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  18Q LOSS MUTATED                                              2
  18Q LOSS WILD-TYPE                                            2
D73V6, multiclass
                                               clus
vv                                              18Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            29
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                1
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         11
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              18Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             115
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                            9
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   2
[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"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     7  38
  18Q LOSS WILD-TYPE  20 111
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7   38
  18Q LOSS WILD-TYPE   20  111
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 7                 20
  YES               38                111
[1] 2 2
[1] FALSE
D73V8, continuous
D73V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  2     3
  18Q LOSS WILD-TYPE                                5    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED                           5
  18Q LOSS WILD-TYPE                        13
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           0    35
  18Q LOSS WILD-TYPE                                         1    95
D73V10, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  5
  ASIAN                                                    3                 12
  BLACK OR AFRICAN AMERICAN                                5                 13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   35                 95
[1] 5 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
  18Q LOSS MUTATED    3 31
  18Q LOSS WILD-TYPE  8 96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   31
  18Q LOSS WILD-TYPE    8   96
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  8
  NOT HISPANIC OR LATINO               31                 96
[1] 2 2
[1] FALSE
D73V12, continuous
D73V13, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   11  4
  18Q LOSS WILD-TYPE 37 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     11    4
  18Q LOSS WILD-TYPE   37   15
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  TUMOR FREE               11                 37
  WITH TUMOR                4                 15
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  18Q LOSS MUTATED         0      3       1            39       2
  18Q LOSS WILD-TYPE       1      7       5           108      10
D73V14, multiclass
               clus
vv              18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       3                  7
  UKRAINE                      1                  5
  UNITED STATES               39                108
  VIETNAM                      2                 10
[1] 5 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                 G1 G2 G3 G4 GX
  18Q LOSS MUTATED    4 18 19  1  3
  18Q LOSS WILD-TYPE 10 65 53  0  2
D73V15, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  G1                4                 10
  G2               18                 65
  G3               19                 53
  G4                1                  0
  GX                3                  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"
D73V16, continuous
D73V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  18Q LOSS MUTATED                                             4
  18Q LOSS WILD-TYPE                                          17
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  18Q LOSS MUTATED                                        1
  18Q LOSS WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  18Q LOSS MUTATED                                                 0
  18Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  18Q LOSS MUTATED                8                  22
  18Q LOSS WILD-TYPE             28                  61
D73V18, multiclass
                                                 clus
vv                                                18Q LOSS 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                                                 8
  LIFELONG NON-SMOKER                                           22
                                                 clus
vv                                                18Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     17
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  28
  LIFELONG NON-SMOKER                                             61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  18Q LOSS MUTATED             4        8             3        2
  18Q LOSS WILD-TYPE          13       29             8        3
D73V20, multiclass
               clus
vv              18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COMBINATION                  4                 13
  EXTERNAL                     8                 29
  EXTERNAL BEAM                3                  8
  INTERNAL                     2                  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"
D73V21, binary
                    cls
clus                 0 1
  18Q LOSS MUTATED   3 1
  18Q LOSS WILD-TYPE 8 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    1
  18Q LOSS WILD-TYPE    8    2
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CGY                3                  8
  GY                 1                  2
[1] 2 2
[1] FALSE
D73V22, continuous
D73V23, continuous
D73V24, continuous
D73V25, continuous
D73V26, continuous
D73V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  18Q LOSS MUTATED                                     0
  18Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  18Q LOSS MUTATED                                     0
  18Q LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  18Q LOSS MUTATED                         2                       0
  18Q LOSS WILD-TYPE                       7                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  18Q LOSS MUTATED                         2
  18Q LOSS WILD-TYPE                       3
D73V28, multiclass
                                     clus
vv                                    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                0                  6
  OTHER LOCATION, SPECIFY                            2                  7
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            2                  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)
  18Q LOSS MUTATED                                               0
  18Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  18Q LOSS MUTATED                                                3
  18Q LOSS WILD-TYPE                                              7
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  18Q LOSS MUTATED                                                                                  15
  18Q LOSS WILD-TYPE                                                                                39
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  18Q LOSS MUTATED                                                                                             20
  18Q LOSS WILD-TYPE                                                                                           57
D73V29, multiclass
                                                                                              clus
vv                                                                                             18Q 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)                          15
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               20
                                                                                              clus
vv                                                                                             18Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                7
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            39
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 57
[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"
D73V30, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   15  9
  18Q LOSS WILD-TYPE 39 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     15    9
  18Q LOSS WILD-TYPE   39   50
         clus
vv        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ABSENT                15                 39
  PRESENT                9                 50
[1] 2 2
[1] FALSE
D73V31, continuous
D73V32, continuous
D73V33, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    8 17
  18Q LOSS WILD-TYPE 27 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      8   17
  18Q LOSS WILD-TYPE   27   64
                                          clus
vv                                         18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    8                 27
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               17                 64
[1] 2 2
[1] FALSE
D73V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  18Q LOSS MUTATED       1                   24                   2
  18Q LOSS WILD-TYPE     2                   89                   3
D73V35, multiclass
                      clus
vv                     18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  OTHER                               1                  2
  RADICAL HYSTERECTOMY               24                 89
  SIMPLE HYSTERECTOMY                 2                  3
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  18Q LOSS MUTATED              3          16          8
  18Q LOSS WILD-TYPE            5          24         32
D73V36, multiclass
              clus
vv             18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CURRENT USER                3                  5
  FORMER USER                16                 24
  NEVER USED                  8                 32
[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
D73V38, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   21  0
  18Q LOSS WILD-TYPE 52 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     21    0
  18Q LOSS WILD-TYPE   52   14
         clus
vv        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ABSENT                21                 52
  PRESENT                0                 14
[1] 2 2
[1] FALSE
D73V39, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  8 
        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-HM-A3JK         TCGA-JW-A852 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  18Q LOSS MUTATED     1    0   4   16    2  0   1    2    1   2   1  0  2
  18Q LOSS WILD-TYPE   1    1  18   35   19  3   5    4    7  11   1  1  5
D73V40, multiclass
      clus
vv     18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1A                 1                  1
  T1A1                0                  1
  T1B                 4                 18
  T1B1               16                 35
  T1B2                2                 19
  T2                  0                  3
  T2A                 1                  5
  T2A1                2                  4
  T2A2                1                  7
  T2B                 2                 11
  T3B                 1                  1
  T4                  0                  1
  TX                  2                  5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V41, continuous

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    20   6
  19P LOSS WILD-TYPE 117  26
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                26                143 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 26 
$`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-A1MJ TCGA-C5-A1MN TCGA-C5-A7CO TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DS-A0VN 
        0.46        40.93        73.41         9.34         2.73       118.65 
TCGA-EA-A1QT TCGA-EA-A3Y4 TCGA-EA-A411 TCGA-EA-A439 TCGA-EK-A2IP TCGA-EK-A2RJ 
       12.36        14.50         1.35        14.50         6.64         1.18 
TCGA-EK-A3GJ TCGA-EX-A69L TCGA-FU-A23L TCGA-IR-A3LC TCGA-JW-A5VK TCGA-PN-A8MA 
        0.10         4.47        23.84       117.40        20.48         2.96 
TCGA-Q1-A6DT TCGA-RA-A741 
        3.39         3.88 

$`19P LOSS 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-A1BL TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 
      144.16       177.04       173.29        82.85        19.86        67.46 
TCGA-C5-A1M7 TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MP 
       46.32        53.16        38.99        35.61         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         0.82        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 
      182.93        25.35       101.82       134.33        15.48         9.67 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-DR-A0ZL 
       17.19        85.55        60.69        94.95        13.61        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18         7.33         8.28         0.76         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A410 TCGA-EA-A43B 
        0.82         0.62        13.05         1.18         1.35         1.81 
TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 
       12.66        12.82         0.26        14.89         1.48        13.91 
TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ 
        0.69        14.99        14.96        13.58        13.48        12.59 
TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       45.96         0.53         0.59         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK 
        0.36        23.70         2.24         0.10         0.07         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69M 
        0.03        20.35         7.92         6.94        14.70         6.12 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22         0.92         2.17         0.66         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 
        1.97         1.12        25.41        21.67        20.78        14.93 
TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH 
        4.11       147.39       137.16        66.81        96.95        78.71 
TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ 
       81.96        26.56        36.36        14.43        16.64        19.33 
TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX 
       15.58        10.06         5.13         0.10         0.89         0.07 
TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE 
        0.82        13.87         0.03         5.42        29.72         0.07 
TCGA-MY-A5BF TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        4.34         3.72         3.45         5.85         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59        11.67        93.99 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.10               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            118.65             182.93 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             13.43              13.58 
[1] "0.1 - 118.7 (13.4)" "0.0 - 182.9 (13.6)"
[1] "hr=" "1.4"
D74V2, continuous
                    vv
clus                 T1 T2+T3+T4
  19P LOSS MUTATED   14        5
  19P LOSS WILD-TYPE 83       34
D74V3, multiclass
          clus
vv         19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                     14                 83
  T2+T3+T4                5                 34
[1] 2 2
[1] FALSE
D74V4, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   16  2
  19P LOSS WILD-TYPE 71 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     16    2
  19P LOSS WILD-TYPE   71   38
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               16                 71
  1                2                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19P LOSS MUTATED   12  0  7
  19P LOSS WILD-TYPE 60  3 58
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               12                 60
  M1                0                  3
  MX                7                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED               0                               25
  19P LOSS WILD-TYPE             2                              119
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19P LOSS MUTATED                                               0
  19P LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19P LOSS MUTATED                                     4
  19P LOSS WILD-TYPE                                  16
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19P LOSS MUTATED                                           0
  19P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19P LOSS MUTATED                                              1
  19P LOSS WILD-TYPE                                            3
D74V6, multiclass
                                               clus
vv                                              19P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            25
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              19P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             119
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     6  24
  19P LOSS WILD-TYPE  21 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6   24
  19P LOSS WILD-TYPE   21  125
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 6                 21
  YES               24                125
[1] 2 2
[1] FALSE
D74V8, continuous
D74V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     2
  19P LOSS WILD-TYPE                                7    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED                           2
  19P LOSS WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           1    25
  19P LOSS WILD-TYPE                                         0   105
D74V10, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    2                 13
  BLACK OR AFRICAN AMERICAN                                2                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   25                105
[1] 5 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
  19P LOSS MUTATED     1  21
  19P LOSS WILD-TYPE  10 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   21
  19P LOSS WILD-TYPE   10  106
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               21                106
[1] 2 2
[1] FALSE
D74V12, continuous
D74V13, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   11  3
  19P LOSS WILD-TYPE 37 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     11    3
  19P LOSS WILD-TYPE   37   16
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  TUMOR FREE               11                 37
  WITH TUMOR                3                 16
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  19P LOSS MUTATED         1      2       1            25       1
  19P LOSS WILD-TYPE       0      8       5           122      11
D74V14, multiclass
               clus
vv              19P LOSS MUTATED 19P LOSS WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       2                  8
  UKRAINE                      1                  5
  UNITED STATES               25                122
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  19P LOSS MUTATED    1 11 15  0  2
  19P LOSS WILD-TYPE 13 72 57  1  3
D74V15, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  G1                1                 13
  G2               11                 72
  G3               15                 57
  G4                0                  1
  GX                2                  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"
D74V16, continuous
D74V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19P LOSS MUTATED                                             2
  19P LOSS WILD-TYPE                                          19
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  19P LOSS MUTATED                                        2
  19P LOSS WILD-TYPE                                      6
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  19P LOSS MUTATED                                                 0
  19P LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19P LOSS MUTATED                3                  15
  19P LOSS WILD-TYPE             33                  68
D74V18, multiclass
                                                 clus
vv                                                19P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    2
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         2
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 3
  LIFELONG NON-SMOKER                                           15
                                                 clus
vv                                                19P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     19
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           6
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  33
  LIFELONG NON-SMOKER                                             68
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  19P LOSS MUTATED             3        6             3        2
  19P LOSS WILD-TYPE          14       31             8        3
D74V20, multiclass
               clus
vv              19P LOSS MUTATED 19P LOSS WILD-TYPE
  COMBINATION                  3                 14
  EXTERNAL                     6                 31
  EXTERNAL BEAM                3                  8
  INTERNAL                     2                  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"
D74V21, binary
                    cls
clus                 0 1
  19P LOSS MUTATED   2 1
  19P LOSS WILD-TYPE 9 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    1
  19P LOSS WILD-TYPE    9    2
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  CGY                2                  9
  GY                 1                  2
[1] 2 2
[1] FALSE
D74V22, continuous
D74V23, continuous
D74V24, continuous
D74V25, continuous
D74V26, continuous
D74V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  19P LOSS MUTATED                                     0
  19P LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  19P LOSS MUTATED                                     1
  19P LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  19P LOSS MUTATED                         1                       0
  19P LOSS WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19P LOSS MUTATED                         0
  19P LOSS WILD-TYPE                       5
D74V28, multiclass
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 21 
        TCGA-C5-A0TN         TCGA-C5-A1BE         TCGA-C5-A1BM 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-DR-A0ZM         TCGA-DS-A0VK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A3LQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A50E         TCGA-EK-A2RN         TCGA-EK-A2RO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A449         TCGA-FU-A3EO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3LH         TCGA-IR-A3LI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-MU-A8JM         TCGA-UC-A7PD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
                    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                                                0
  19P LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19P LOSS MUTATED                                                                                   8
  19P LOSS WILD-TYPE                                                                                46
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19P LOSS MUTATED                                                                                             12
  19P LOSS WILD-TYPE                                                                                           65
D74V29, multiclass
                                                                                              clus
vv                                                                                             19P 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)                           8
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               12
                                                                                              clus
vv                                                                                             19P LOSS WILD-TYPE
  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)                            46
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 65
[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"
D74V30, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    8  9
  19P LOSS WILD-TYPE 46 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8    9
  19P LOSS WILD-TYPE   46   50
         clus
vv        19P LOSS MUTATED 19P LOSS WILD-TYPE
  ABSENT                 8                 46
  PRESENT                9                 50
[1] 2 2
[1] FALSE
D74V31, continuous
D74V32, continuous
D74V33, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    3 15
  19P LOSS WILD-TYPE 32 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3   15
  19P LOSS WILD-TYPE   32   66
                                          clus
vv                                         19P LOSS MUTATED 19P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               15                 66
[1] 2 2
[1] FALSE
D74V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  19P LOSS MUTATED       0                   16                   1
  19P LOSS WILD-TYPE     3                   97                   4
D74V35, multiclass
                      clus
vv                     19P LOSS MUTATED 19P LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               16                 97
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19P LOSS MUTATED              1           7          6
  19P LOSS WILD-TYPE            7          33         34
D74V36, multiclass
              clus
vv             19P LOSS MUTATED 19P LOSS WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 7                 33
  NEVER USED                  6                 34
[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
D74V38, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   11  3
  19P LOSS WILD-TYPE 62 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     11    3
  19P LOSS WILD-TYPE   62   11
         clus
vv        19P LOSS MUTATED 19P LOSS WILD-TYPE
  ABSENT                11                 62
  PRESENT                3                 11
[1] 2 2
[1] FALSE
D74V39, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                  7 
        TCGA-C5-A1MH         TCGA-C5-A1MP         TCGA-EK-A2RO 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-JW-A852         TCGA-MU-A51Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MU-A8JM 
"19P LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  19P LOSS MUTATED     0    0   3    8    3  0   1    2    0   1   1  0  1
  19P LOSS WILD-TYPE   2    1  19   43   18  3   5    4    8  12   1  1  6
D74V40, multiclass
      clus
vv     19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 3                 19
  T1B1                8                 43
  T1B2                3                 18
  T2                  0                  3
  T2A                 1                  5
  T2A1                2                  4
  T2A2                0                  8
  T2B                 1                 12
  T3B                 1                  1
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V41, continuous

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    10   3
  19Q LOSS WILD-TYPE 127  29
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                156 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 29 
$`19Q LOSS MUTATED`
TCGA-C5-A1M6 TCGA-C5-A1M8 TCGA-C5-A1M9 TCGA-C5-A1MJ TCGA-C5-A7X8 TCGA-DS-A0VN 
       31.40        30.21        35.01         0.46         2.73       118.65 
TCGA-EA-A1QT TCGA-EK-A2IP TCGA-EK-A3GJ TCGA-FU-A23L TCGA-IR-A3LC TCGA-JW-A5VK 
       12.36         6.64         0.10        23.84       117.40        20.48 
TCGA-Q1-A6DT 
        3.39 

$`19Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH 
       19.86        67.46        46.32        57.73        53.16        38.99 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT 
       35.61         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         0.82 
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       182.93        25.35 
TCGA-C5-A7CJ TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC 
      101.82       134.33        15.48         9.67        73.41        17.19 
TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-DR-A0ZL 
       85.55        60.69        94.95         9.34        13.61        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ 
       58.88        36.76         2.66       117.99        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR 
       16.18         7.33         8.28         0.76         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 
        0.82         0.62        13.05         1.18        14.50         1.35 
TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
        1.35        14.50         1.81        12.66        12.82         0.26 
TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF 
       14.89         1.48        13.91         0.69        14.99        14.96 
TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2PG TCGA-EK-A2R7 
       13.58        13.48        12.59        45.96         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL 
        0.07         4.04         0.03         0.36         1.18        23.70 
TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        2.24         0.10         0.07         0.10         0.03        20.35 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K 
        7.92         6.94        14.70         4.47         6.12         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        0.92         2.17         0.66         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV 
        1.48         0.82         3.52         1.35         1.32         1.97 
TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 
        1.12        25.41        21.67        20.78        14.93         4.11 
TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      147.39       137.16        66.81        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VL 
       26.56        36.36        14.43        16.64        19.33        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       10.06         5.13         0.10         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW 
        2.96         3.72         3.45         5.85         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.10               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            118.65             182.93 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             20.48              13.53 
[1] "0.1 - 118.7 (20.5)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.1"
D75V2, continuous
                    vv
clus                 T1 T2+T3+T4
  19Q LOSS MUTATED    8        3
  19Q LOSS WILD-TYPE 89       36
D75V3, multiclass
          clus
vv         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                      8                 89
  T2+T3+T4                3                 36
[1] 2 2
[1] FALSE
D75V4, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    8  2
  19Q LOSS WILD-TYPE 79 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8    2
  19Q LOSS WILD-TYPE   79   38
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                8                 79
  1                2                 38
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19Q LOSS MUTATED    5  0  6
  19Q LOSS WILD-TYPE 67  3 59
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                5                 67
  M1                0                  3
  MX                6                 59
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED               0                               11
  19Q LOSS WILD-TYPE             2                              133
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  19Q LOSS MUTATED                                               0
  19Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  19Q LOSS MUTATED                                     3
  19Q LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  19Q LOSS MUTATED                                           0
  19Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  19Q LOSS MUTATED                                              1
  19Q LOSS WILD-TYPE                                            3
D75V6, multiclass
                                               clus
vv                                              19Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            11
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 1
                                               clus
vv                                              19Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             133
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   3
[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"
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     4  11
  19Q LOSS WILD-TYPE  23 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4   11
  19Q LOSS WILD-TYPE   23  138
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 4                 23
  YES               11                138
[1] 2 2
[1] FALSE
D75V8, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LS         TCGA-C5-A2LT 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FU-A770         TCGA-HM-A4S6         TCGA-HM-A6W2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-MU-A5YI         TCGA-MU-A8JM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741         TCGA-UC-A7PD 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D75V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     0
  19Q LOSS WILD-TYPE                                7    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED                           1
  19Q LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           1    13
  19Q LOSS WILD-TYPE                                         0   117
D75V10, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  7
  ASIAN                                                    0                 15
  BLACK OR AFRICAN AMERICAN                                1                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   13                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"
D75V11, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1   7
  19Q LOSS WILD-TYPE  10 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    7
  19Q LOSS WILD-TYPE   10  120
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO                7                120
[1] 2 2
[1] FALSE
D75V12, continuous
D75V13, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    6  2
  19Q LOSS WILD-TYPE 42 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    2
  19Q LOSS WILD-TYPE   42   17
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  TUMOR FREE                6                 42
  WITH TUMOR                2                 17
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  19Q LOSS MUTATED         0      1       0            14       0
  19Q LOSS WILD-TYPE       1      9       6           133      12
D75V14, multiclass
               clus
vv              19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES               14                133
  VIETNAM                      0                 12
[1] 5 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                 G1 G2 G3 G4 GX
  19Q LOSS MUTATED    0  7  7  0  1
  19Q LOSS WILD-TYPE 14 76 65  1  4
D75V15, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  G1                0                 14
  G2                7                 76
  G3                7                 65
  G4                0                  1
  GX                1                  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"
D75V16, continuous
D75V17, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 51 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LS         TCGA-C5-A2LT 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A5RQ         TCGA-DS-A7WF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-FU-A5XV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FU-A770         TCGA-HM-A4S6         TCGA-HM-A6W2 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LB         TCGA-IR-A3LH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-MU-A5YI         TCGA-MU-A8JM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741         TCGA-UC-A7PD 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  19Q LOSS MUTATED                                             0
  19Q LOSS WILD-TYPE                                          21
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  19Q LOSS MUTATED                                        1
  19Q LOSS WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  19Q LOSS MUTATED                                                 0
  19Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  19Q LOSS MUTATED                1                  10
  19Q LOSS WILD-TYPE             35                  73
D75V18, multiclass
                                                 clus
vv                                                19Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 1
  LIFELONG NON-SMOKER                                           10
                                                 clus
vv                                                19Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  35
  LIFELONG NON-SMOKER                                             73
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V19, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 46 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A2LS         TCGA-C5-A2LT 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CL         TCGA-C5-A7CO 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-DR-A0ZM         TCGA-DS-A5RQ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EA-A556         TCGA-EX-A1H5         TCGA-FU-A2QG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3TQ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FU-A3TX         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FU-A5XV         TCGA-FU-A770         TCGA-HM-A4S6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-MU-A5YI 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-Q1-A6DW         TCGA-RA-A741 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-UC-A7PD 
"19Q LOSS WILD-TYPE" 
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  19Q LOSS MUTATED             1        3             3        0
  19Q LOSS WILD-TYPE          16       34             8        5
D75V20, multiclass
               clus
vv              19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COMBINATION                  1                 16
  EXTERNAL                     3                 34
  EXTERNAL BEAM                3                  8
  INTERNAL                     0                  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"
D75V21, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  0
  19Q LOSS WILD-TYPE 10  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    0
  19Q LOSS WILD-TYPE   10    3
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CGY                1                 10
  GY                 0                  3
[1] 2 2
[1] FALSE
D75V22, continuous
D75V23, continuous
D75V24, continuous
D75V25, continuous
D75V26, continuous
D75V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  19Q LOSS MUTATED                                     0
  19Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  19Q LOSS MUTATED                                     0
  19Q LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  19Q LOSS MUTATED                         1                       0
  19Q LOSS WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  19Q LOSS MUTATED                         0
  19Q LOSS WILD-TYPE                       5
D75V28, multiclass
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 22 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A2LX         TCGA-DR-A0ZM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-EA-A50E         TCGA-EK-A2RN 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-EX-A1H5         TCGA-EX-A449 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-HM-A4S6         TCGA-IR-A3LH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IR-A3LI         TCGA-IR-A3LK         TCGA-MU-A8JM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-UC-A7PD 
"19Q LOSS WILD-TYPE" 
                    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                                                0
  19Q LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  19Q LOSS MUTATED                                                                                   6
  19Q LOSS WILD-TYPE                                                                                48
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  19Q LOSS MUTATED                                                                                              4
  19Q LOSS WILD-TYPE                                                                                           73
D75V29, multiclass
                                                                                              clus
vv                                                                                             19Q 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)                           6
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                4
                                                                                              clus
vv                                                                                             19Q LOSS WILD-TYPE
  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)                            48
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 73
[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"
D75V30, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    5  5
  19Q LOSS WILD-TYPE 49 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5    5
  19Q LOSS WILD-TYPE   49   54
         clus
vv        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ABSENT                 5                 49
  PRESENT                5                 54
[1] 2 2
[1] FALSE
D75V31, continuous
D75V32, continuous
D75V33, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  4
  19Q LOSS WILD-TYPE 33 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    4
  19Q LOSS WILD-TYPE   33   77
                                          clus
vv                                         19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    2                 33
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                4                 77
[1] 2 2
[1] FALSE
D75V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  19Q LOSS MUTATED       0                   10                   0
  19Q LOSS WILD-TYPE     3                  103                   5
D75V35, multiclass
                      clus
vv                     19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               10                103
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  19Q LOSS MUTATED              1           3          3
  19Q LOSS WILD-TYPE            7          37         37
D75V36, multiclass
              clus
vv             19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 3                 37
  NEVER USED                  3                 37
[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, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    8  1
  19Q LOSS WILD-TYPE 65 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8    1
  19Q LOSS WILD-TYPE   65   13
         clus
vv        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ABSENT                 8                 65
  PRESENT                1                 13
[1] 2 2
[1] FALSE
D75V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  19Q LOSS MUTATED     0    0   2    4    2  0   1    1    0   0   1  0  1
  19Q LOSS WILD-TYPE   2    1  20   47   19  3   5    5    8  13   1  1  6
D75V40, multiclass
      clus
vv     19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 2                 20
  T1B1                4                 47
  T1B2                2                 19
  T2                  0                  3
  T2A                 1                  5
  T2A1                1                  5
  T2A2                0                  8
  T2B                 0                 13
  T3B                 1                  1
  T4                  0                  1
  TX                  1                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V41, continuous

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     7   2
  20P LOSS WILD-TYPE 130  30
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                160 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 30 
$`20P LOSS MUTATED`
TCGA-BI-A0VR TCGA-EA-A1QT TCGA-EK-A2H0 TCGA-EX-A1H6 TCGA-FU-A3HY TCGA-FU-A770 
       49.48        12.36        45.96         7.92         0.66         1.12 
TCGA-IR-A3LB TCGA-JW-A5VI TCGA-UC-A7PD 
       66.81        16.64        11.67 

$`20P LOSS WILD-TYPE`
TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI 
       57.04        23.67        11.44        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-A1M9 TCGA-C5-A1ME 
       67.46        31.40        46.32        30.21        35.01        57.73 
TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI TCGA-C5-A1MJ TCGA-C5-A1MK TCGA-C5-A1MN 
       53.16        38.99        35.61         0.46         2.43        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         0.82        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       182.93        25.35       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
        9.67        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        9.34        13.61         2.73        87.75        58.88        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF 
        2.66       117.99       118.65        22.98        16.83        16.18 
TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        7.33         8.28         0.76         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 
        0.62        13.05         1.18        14.50         1.35         1.35 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50         1.81        12.66        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB 
       13.48        12.59         6.64         0.53         0.59         0.07 
TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        4.04         0.03         0.36         1.18        23.70         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 
        0.10         0.07         0.10         0.10         0.03        20.35 
TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L 
        6.94        14.70         4.47         6.12         1.22        23.84 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX 
        0.92         2.17         1.02         1.45         1.58         1.48 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-HG-A2PA 
        0.82         3.52         1.35         1.32         1.97        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         4.11       147.39       137.16 
TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL 
      117.40        96.95        78.71        81.96        26.56        36.36 
TCGA-JW-A5VG TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       14.43        19.33        20.48        15.58        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        0.10         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         2.96         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.45         5.85         3.39         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        6.25        19.59         3.88        93.99 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.66               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             66.81             182.93 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            12.360             13.595 
[1] "0.7 - 66.8 (12.4)"  "0.0 - 182.9 (13.6)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 T1 T2+T3+T4
  20P LOSS MUTATED    6        3
  20P LOSS WILD-TYPE 91       36
D76V3, multiclass
          clus
vv         20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                      6                 91
  T2+T3+T4                3                 36
[1] 2 2
[1] FALSE
D76V4, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    5  3
  20P LOSS WILD-TYPE 82 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5    3
  20P LOSS WILD-TYPE   82   37
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                5                 82
  1                3                 37
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20P LOSS MUTATED    5  0  4
  20P LOSS WILD-TYPE 67  3 61
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                5                 67
  M1                0                  3
  MX                4                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED               0                                8
  20P LOSS WILD-TYPE             2                              136
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20P LOSS MUTATED                                               1
  20P LOSS WILD-TYPE                                             3
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20P LOSS MUTATED                                     2
  20P LOSS WILD-TYPE                                  18
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20P LOSS MUTATED                                           0
  20P LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20P LOSS MUTATED                                              0
  20P LOSS WILD-TYPE                                            4
D76V6, multiclass
                                               clus
vv                                              20P LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             8
  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                                              20P LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             136
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  3
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  11
  20P LOSS WILD-TYPE  27 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   11
  20P LOSS WILD-TYPE   27  138
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                 27
  YES               11                138
[1] 2 2
[1] FALSE
D76V8, continuous
D76V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  2     1
  20P LOSS WILD-TYPE                                5    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED                           0
  20P LOSS WILD-TYPE                        18
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           0     8
  20P LOSS WILD-TYPE                                         1   122
D76V10, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  5
  ASIAN                                                    1                 14
  BLACK OR AFRICAN AMERICAN                                0                 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    8                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"
D76V11, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1   6
  20P LOSS WILD-TYPE  10 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    6
  20P LOSS WILD-TYPE   10  121
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO                6                121
[1] 2 2
[1] FALSE
D76V12, continuous
D76V13, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    1  0
  20P LOSS WILD-TYPE 47 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    0
  20P LOSS WILD-TYPE   47   19
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  TUMOR FREE                1                 47
  WITH TUMOR                0                 19
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  20P LOSS MUTATED         0      1       0             9       1
  20P LOSS WILD-TYPE       1      9       6           138      11
D76V14, multiclass
               clus
vv              20P LOSS MUTATED 20P LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       1                  9
  UKRAINE                      0                  6
  UNITED STATES                9                138
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  20P LOSS MUTATED    1  6  4  0  0
  20P LOSS WILD-TYPE 13 77 68  1  5
D76V15, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  G1                1                 13
  G2                6                 77
  G3                4                 68
  G4                0                  1
  GX                0                  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"
D76V16, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 23 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MH 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A7CM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-DS-A3LQ         TCGA-EX-A69M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3TX         TCGA-FU-A3WB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-HM-A4S6         TCGA-IR-A3L7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-MU-A5YI         TCGA-MU-A8JM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D76V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20P LOSS MUTATED                                             1
  20P LOSS WILD-TYPE                                          20
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  20P LOSS MUTATED                                        1
  20P LOSS WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  20P LOSS MUTATED                                                 0
  20P LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20P LOSS MUTATED                4                   3
  20P LOSS WILD-TYPE             32                  80
D76V18, multiclass
                                                 clus
vv                                                20P LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    1
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         1
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 4
  LIFELONG NON-SMOKER                                            3
                                                 clus
vv                                                20P LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     20
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  32
  LIFELONG NON-SMOKER                                             80
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  20P LOSS MUTATED             0        2             0        1
  20P LOSS WILD-TYPE          17       35            11        4
D76V20, multiclass
               clus
vv              20P LOSS MUTATED 20P LOSS WILD-TYPE
  COMBINATION                  0                 17
  EXTERNAL                     2                 35
  EXTERNAL BEAM                0                 11
  INTERNAL                     1                  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"
D76V21, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    0  0
  20P LOSS WILD-TYPE 11  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    0
  20P LOSS WILD-TYPE   11    3
D76V22, continuous
D76V23, continuous
D76V24, continuous
D76V25, continuous
D76V26, continuous
D76V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  20P LOSS MUTATED                                     0
  20P LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  20P LOSS MUTATED                                     0
  20P LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  20P LOSS MUTATED                         1                       0
  20P LOSS WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20P LOSS MUTATED                         0
  20P LOSS WILD-TYPE                       5
D76V28, multiclass
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 22 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A2LX         TCGA-DR-A0ZM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A50E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EK-A2RN         TCGA-EK-A2RO         TCGA-EX-A1H5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EX-A449         TCGA-FU-A3EO         TCGA-HM-A4S6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MU-A8JM 
"20P LOSS WILD-TYPE" 
                    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                                                0
  20P LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20P LOSS MUTATED                                                                                   3
  20P LOSS WILD-TYPE                                                                                51
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20P LOSS MUTATED                                                                                              6
  20P LOSS WILD-TYPE                                                                                           71
D76V29, multiclass
                                                                                              clus
vv                                                                                             20P 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)                           3
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                6
                                                                                              clus
vv                                                                                             20P LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  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)                 71
[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"
D76V30, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    3  4
  20P LOSS WILD-TYPE 51 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    4
  20P LOSS WILD-TYPE   51   55
         clus
vv        20P LOSS MUTATED 20P LOSS WILD-TYPE
  ABSENT                 3                 51
  PRESENT                4                 55
[1] 2 2
[1] FALSE
D76V31, continuous
D76V32, continuous
D76V33, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    1  5
  20P LOSS WILD-TYPE 34 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    5
  20P LOSS WILD-TYPE   34   76
                                          clus
vv                                         20P LOSS MUTATED 20P LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    1                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                5                 76
[1] 2 2
[1] FALSE
D76V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  20P LOSS MUTATED       1                    6                   0
  20P LOSS WILD-TYPE     2                  107                   5
D76V35, multiclass
                      clus
vv                     20P LOSS MUTATED 20P LOSS WILD-TYPE
  OTHER                               1                  2
  RADICAL HYSTERECTOMY                6                107
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20P LOSS MUTATED              1           4          2
  20P LOSS WILD-TYPE            7          36         38
D76V36, multiclass
              clus
vv             20P LOSS MUTATED 20P LOSS WILD-TYPE
  CURRENT USER                1                  7
  FORMER USER                 4                 36
  NEVER USED                  2                 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"
D76V37, continuous
D76V38, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    4  1
  20P LOSS WILD-TYPE 69 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4    1
  20P LOSS WILD-TYPE   69   13
         clus
vv        20P LOSS MUTATED 20P LOSS WILD-TYPE
  ABSENT                 4                 69
  PRESENT                1                 13
[1] 2 2
[1] FALSE
D76V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  20P LOSS MUTATED     0    0   3    2    1  0   0    0    1   2   0  0  0
  20P LOSS WILD-TYPE   2    1  19   49   20  3   6    6    7  11   2  1  7
D76V40, multiclass
      clus
vv     20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 3                 19
  T1B1                2                 49
  T1B2                1                 20
  T2                  0                  3
  T2A                 0                  6
  T2A1                0                  6
  T2A2                1                  7
  T2B                 2                 11
  T3B                 0                  2
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V41, continuous

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     2   1
  20Q LOSS WILD-TYPE 135  31
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                166 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 31 
$`20Q LOSS MUTATED`
TCGA-FU-A40J TCGA-HG-A2PA TCGA-UC-A7PD 
        1.35        25.41        11.67 

$`20Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BF 
       49.48        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-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-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HD TCGA-C5-A3HE 
       78.35       100.14        38.43         0.82        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       182.93        25.35       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48         9.67        73.41        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZL TCGA-DR-A0ZM 
       94.95         9.34        13.61         2.73        87.75        58.88 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-DS-A5RQ 
       36.76         2.66       117.99       118.65        22.98        16.83 
TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A1QT TCGA-EA-A3HQ 
       16.18         7.33         8.28         0.76        12.36         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE TCGA-EA-A3Y4 
        1.32         0.82         0.62        13.05         1.18        14.50 
TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA 
        1.35         1.35        14.50         1.81        12.66        12.82 
TCGA-EA-A50E TCGA-EA-A556 TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE 
        0.26        14.89         1.48        13.91         0.69        14.99 
TCGA-EA-A5ZF TCGA-EA-A6QX TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP 
       14.96        13.58        13.48        12.59        45.96         6.64 
TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RE 
        0.53         0.59         0.07         4.04         0.03         0.36 
TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        1.18        23.70         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 
        0.10         0.03        20.35         7.92         6.94        14.70 
TCGA-EX-A69L TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        4.47         6.12         1.22        23.84         0.92         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB 
        0.66         1.02         1.45         1.58         1.48         0.82 
TCGA-FU-A3YQ TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HM-A3JJ TCGA-HM-A3JK 
        3.52         1.32         1.97         1.12        21.67        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC 
       14.93         4.11       147.39       137.16        66.81       117.40 
TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VG 
       96.95        78.71        81.96        26.56        36.36        14.43 
TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL TCGA-JW-A69B TCGA-JW-A852 
       16.64        19.33        20.48        15.58        10.06         5.13 
TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        0.10         0.89         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF TCGA-PN-A8MA TCGA-Q1-A5R1 
        5.42        29.72         0.07         4.34         2.96         3.72 
TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P 
        3.45         5.85         3.39         3.72         5.75         4.80 
TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PF 
        6.25        19.59         3.88        93.99 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              1.35               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             25.41             182.93 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            11.670             13.595 
[1] "1.4 - 25.4 (11.7)"  "0.0 - 182.9 (13.6)"
[1] "hr=" "3.5"
D77V2, continuous
                    vv
clus                 T1 T2+T3+T4
  20Q LOSS MUTATED    2        1
  20Q LOSS WILD-TYPE 95       38
D77V3, multiclass
          clus
vv         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                      2                 95
  T2+T3+T4                1                 38
[1] 2 2
[1] FALSE
D77V4, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    2  1
  20Q LOSS WILD-TYPE 85 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    1
  20Q LOSS WILD-TYPE   85   39
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                2                 85
  1                1                 39
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20Q LOSS MUTATED    2  0  1
  20Q LOSS WILD-TYPE 70  3 64
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                2                 70
  M1                0                  3
  MX                1                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED               0                                3
  20Q LOSS WILD-TYPE             2                              141
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  20Q LOSS MUTATED                                               0
  20Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  20Q LOSS MUTATED                                     1
  20Q LOSS WILD-TYPE                                  19
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  20Q LOSS MUTATED                                           0
  20Q LOSS WILD-TYPE                                         2
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  20Q LOSS MUTATED                                              0
  20Q LOSS WILD-TYPE                                            4
D77V6, multiclass
                                               clus
vv                                              20Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                             3
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          1
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    0
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              20Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             141
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           19
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      2
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D77V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   4
  20Q LOSS WILD-TYPE  27 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    4
  20Q LOSS WILD-TYPE   27  145
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 0                 27
  YES                4                145
[1] 2 2
[1] FALSE
D77V8, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LS         TCGA-C5-A2LT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-DR-A0ZM         TCGA-DS-A5RQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-EA-A556         TCGA-EX-A1H5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A5XV         TCGA-FU-A770         TCGA-HM-A4S6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"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-RA-A741 
"20Q LOSS WILD-TYPE" 
D77V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  1     0
  20Q LOSS WILD-TYPE                                6    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q LOSS MUTATED                           0
  20Q LOSS WILD-TYPE                        18
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q LOSS MUTATED                                           0     3
  20Q LOSS WILD-TYPE                                         1   127
D77V10, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  6
  ASIAN                                                    0                 15
  BLACK OR AFRICAN AMERICAN                                0                 18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                    3                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"
D77V11, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   2
  20Q LOSS WILD-TYPE  11 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    2
  20Q LOSS WILD-TYPE   11  125
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 11
  NOT HISPANIC OR LATINO                2                125
[1] 2 2
[1] FALSE
D77V12, continuous
D77V13, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    0  0
  20Q LOSS WILD-TYPE 48 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    0
  20Q LOSS WILD-TYPE   48   19
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  20Q LOSS MUTATED         0      0       0             4       0
  20Q LOSS WILD-TYPE       1     10       6           143      12
D77V14, multiclass
               clus
vv              20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       0                 10
  UKRAINE                      0                  6
  UNITED STATES                4                143
  VIETNAM                      0                 12
[1] 5 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                 G1 G2 G3 G4 GX
  20Q LOSS MUTATED    0  3  1  0  0
  20Q LOSS WILD-TYPE 14 80 71  1  5
D77V15, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  G1                0                 14
  G2                3                 80
  G3                1                 71
  G4                0                  1
  GX                0                  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"
D77V16, continuous
D77V17, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 52 
        TCGA-BI-A0VR         TCGA-C5-A1BF         TCGA-C5-A1BI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BJ         TCGA-C5-A1BL         TCGA-C5-A1BN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M7         TCGA-C5-A1ME 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MH         TCGA-C5-A1MI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LS         TCGA-C5-A2LT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CK         TCGA-C5-A7CL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CO         TCGA-C5-A7UE         TCGA-C5-A7UI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-DR-A0ZM         TCGA-DS-A5RQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-EA-A556         TCGA-EX-A1H5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A5XV         TCGA-FU-A770         TCGA-HM-A4S6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-JW-A5VI         TCGA-JW-A5VK 
"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-RA-A741 
"20Q LOSS WILD-TYPE" 
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  20Q LOSS MUTATED                                             0
  20Q LOSS WILD-TYPE                                          21
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  20Q LOSS MUTATED                                        0
  20Q LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  20Q LOSS MUTATED                                                 0
  20Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  20Q LOSS MUTATED                2                   1
  20Q LOSS WILD-TYPE             34                  82
D77V18, multiclass
                                                 clus
vv                                                20Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 2
  LIFELONG NON-SMOKER                                            1
                                                 clus
vv                                                20Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  34
  LIFELONG NON-SMOKER                                             82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V19, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 47 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1ME         TCGA-C5-A1MF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A2LS         TCGA-C5-A2LT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2LV         TCGA-C5-A2LX         TCGA-C5-A2LZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CJ         TCGA-C5-A7CL         TCGA-C5-A7CO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7X8         TCGA-DR-A0ZM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A5RQ         TCGA-EA-A556         TCGA-EX-A1H5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3TX         TCGA-FU-A3WB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A5XV         TCGA-FU-A770 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LH         TCGA-JW-A5VI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-MU-A5YI         TCGA-MU-A8JM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Q1-A6DW         TCGA-RA-A741 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  20Q LOSS MUTATED             0        0             0        1
  20Q LOSS WILD-TYPE          17       37            11        4
D77V20, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 69 
        TCGA-C5-A0TN         TCGA-C5-A1BE         TCGA-C5-A1BF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A1BN         TCGA-C5-A1BQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1M6         TCGA-C5-A1M8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M9         TCGA-C5-A1MF         TCGA-C5-A1MH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MK         TCGA-C5-A1MN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2LT         TCGA-C5-A2LX         TCGA-C5-A2LY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2LZ         TCGA-C5-A3HE         TCGA-C5-A3HF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A3HL         TCGA-C5-A7CK         TCGA-C5-A7CL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CM         TCGA-C5-A7CO         TCGA-C5-A7UE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-C5-A7X5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7X8         TCGA-DR-A0ZM         TCGA-DS-A0VK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-DS-A5RQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A7WH         TCGA-DS-A7WI         TCGA-EA-A3QD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3Y4         TCGA-EA-A44S         TCGA-EA-A4BA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EX-A3L1         TCGA-EX-A449 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-HM-A3JJ         TCGA-HM-A3JK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-HM-A6W2         TCGA-IR-A3L7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LA         TCGA-IR-A3LB         TCGA-IR-A3LC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-IR-A3LI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-IR-A3LL         TCGA-JW-A5VG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-PN-A8MA         TCGA-Q1-A5R2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Q1-A5R3         TCGA-R2-A69V         TCGA-RA-A741 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V21, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    0  0
  20Q LOSS WILD-TYPE 11  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    0
  20Q LOSS WILD-TYPE   11    3
D77V22, continuous
D77V23, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 91 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         TCGA-C5-A1M6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         TCGA-C5-A1M9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MJ         TCGA-C5-A1MK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         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-A2LY         TCGA-C5-A2LZ         TCGA-C5-A2M1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A3HL         TCGA-C5-A7CG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CH         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-C5-A7X8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZL         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-A5RQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A3QD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A3Y4         TCGA-EA-A410 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A44S         TCGA-EA-A556 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EX-A449         TCGA-FU-A2QG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A770         TCGA-HM-A3JK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LC         TCGA-IR-A3LF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LL         TCGA-JW-A5VG         TCGA-JW-A5VI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A5VL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-RA-A741 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-UC-A7PF 
"20Q LOSS WILD-TYPE" 
D77V24, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                103 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BF         TCGA-C5-A1BI         TCGA-C5-A1BJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BL         TCGA-C5-A1BM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BN         TCGA-C5-A1BQ         TCGA-C5-A1M5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M6         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-A1MH         TCGA-C5-A1MI         TCGA-C5-A1MJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MK         TCGA-C5-A1MN         TCGA-C5-A1MP 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2LS         TCGA-C5-A2LT         TCGA-C5-A2LV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2LZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2M1         TCGA-C5-A2M2         TCGA-C5-A3HD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A3HE         TCGA-C5-A3HF         TCGA-C5-A3HL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7CH         TCGA-C5-A7CJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CK         TCGA-C5-A7CL         TCGA-C5-A7CO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7UE         TCGA-C5-A7UH         TCGA-C5-A7UI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7X3         TCGA-C5-A7X8         TCGA-DR-A0ZL 
"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-A5RQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HS         TCGA-EA-A3HT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3QE         TCGA-EA-A3Y4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A44S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-EA-A5ZD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EK-A2IP         TCGA-EK-A2RK         TCGA-EX-A69L 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3TQ         TCGA-FU-A3YQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A57G         TCGA-FU-A770         TCGA-HM-A3JK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HM-A4S6         TCGA-IR-A3L7         TCGA-IR-A3LC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-IR-A3LI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-IR-A3LL         TCGA-JW-A5VG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VJ         TCGA-JW-A5VK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A5VL         TCGA-JW-A69B         TCGA-JW-A852 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MU-A8JM         TCGA-PN-A8MA         TCGA-RA-A741 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-UC-A7PF 
"20Q LOSS WILD-TYPE" 
D77V25, continuous
D77V26, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 98 
        TCGA-BI-A0VS         TCGA-C5-A0TN         TCGA-C5-A1BE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         TCGA-C5-A1M6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         TCGA-C5-A1M9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MJ         TCGA-C5-A1MK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         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-A2LY         TCGA-C5-A2LZ         TCGA-C5-A2M1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A3HL         TCGA-C5-A7CG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CH         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-C5-A7X8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZL         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-A5RQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HS         TCGA-EA-A3HT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3QD         TCGA-EA-A3QE         TCGA-EA-A3Y4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A44S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A4BA         TCGA-EA-A556         TCGA-EA-A5O9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A6QX         TCGA-EK-A2RN         TCGA-EX-A1H6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EX-A449         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3TQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A770         TCGA-HM-A3JJ         TCGA-HM-A3JK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3L7         TCGA-IR-A3LC         TCGA-IR-A3LF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LL         TCGA-JW-A5VG         TCGA-JW-A5VI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A5VJ         TCGA-JW-A5VK         TCGA-JW-A5VL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A69B         TCGA-JW-A852         TCGA-MU-A51Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V27, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 92 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BI         TCGA-C5-A1BJ         TCGA-C5-A1BK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BL         TCGA-C5-A1BM         TCGA-C5-A1BN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BQ         TCGA-C5-A1M5         TCGA-C5-A1M6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M7         TCGA-C5-A1M8         TCGA-C5-A1M9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1ME         TCGA-C5-A1MF         TCGA-C5-A1MH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MJ         TCGA-C5-A1MK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         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-A2LY         TCGA-C5-A2LZ         TCGA-C5-A2M1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A3HF         TCGA-C5-A3HL         TCGA-C5-A7CG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CH         TCGA-C5-A7CJ         TCGA-C5-A7CK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CL         TCGA-C5-A7CO         TCGA-C5-A7UE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7UH         TCGA-C5-A7X3         TCGA-C5-A7X8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZL         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-A5RQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A7WF         TCGA-DS-A7WH         TCGA-DS-A7WI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A1QS         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A3QD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3QE         TCGA-EA-A3Y4         TCGA-EA-A410 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A411         TCGA-EA-A44S         TCGA-EA-A556 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A5O9         TCGA-EX-A69M         TCGA-FU-A2QG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A5XV         TCGA-FU-A770 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HM-A3JK         TCGA-IR-A3L7         TCGA-IR-A3LC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LF         TCGA-IR-A3LH         TCGA-IR-A3LI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LK         TCGA-IR-A3LL         TCGA-JW-A5VG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A5VI         TCGA-JW-A5VJ         TCGA-JW-A5VK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A5VL         TCGA-JW-A69B         TCGA-JW-A852 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-RA-A741         TCGA-UC-A7PF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  20Q LOSS MUTATED                                     0
  20Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  20Q LOSS MUTATED                                     0
  20Q LOSS WILD-TYPE                                   6
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  20Q LOSS MUTATED                         1                       0
  20Q LOSS WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  20Q LOSS MUTATED                         0
  20Q LOSS WILD-TYPE                       5
D77V28, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 22 
        TCGA-BI-A20A         TCGA-C5-A0TN         TCGA-C5-A1BE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1BM         TCGA-C5-A2LX         TCGA-DR-A0ZM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A50E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EK-A2RN         TCGA-EK-A2RO         TCGA-EX-A1H5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EX-A449         TCGA-FU-A3EO         TCGA-HM-A4S6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MU-A8JM 
"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                                                0
  20Q LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  20Q LOSS MUTATED                                                                                   0
  20Q LOSS WILD-TYPE                                                                                54
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  20Q LOSS MUTATED                                                                                              3
  20Q LOSS WILD-TYPE                                                                                           74
D77V29, multiclass
                                                                                              clus
vv                                                                                             20Q 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)                           0
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                3
                                                                                              clus
vv                                                                                             20Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  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)                 74
[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"
D77V30, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    0  3
  20Q LOSS WILD-TYPE 54 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    3
  20Q LOSS WILD-TYPE   54   56
         clus
vv        20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ABSENT                 0                 54
  PRESENT                3                 56
[1] 2 2
[1] FALSE
D77V31, continuous
D77V32, continuous
D77V33, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  1
  20Q LOSS WILD-TYPE 34 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    1
  20Q LOSS WILD-TYPE   34   80
                                          clus
vv                                         20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    1                 34
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA                1                 80
[1] 2 2
[1] FALSE
D77V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  20Q LOSS MUTATED       0                    3                   0
  20Q LOSS WILD-TYPE     3                  110                   5
D77V35, multiclass
                      clus
vv                     20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY                3                110
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  20Q LOSS MUTATED              0           1          0
  20Q LOSS WILD-TYPE            8          39         40
D77V36, multiclass
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 87 
        TCGA-C5-A1BI         TCGA-C5-A1BL         TCGA-C5-A1BN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A1M6         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-A1MN         TCGA-C5-A2LT         TCGA-C5-A2LV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2LX         TCGA-C5-A2LY         TCGA-C5-A2M1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A2M2         TCGA-C5-A3HD         TCGA-C5-A3HL 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-C5-A7CG         TCGA-C5-A7UH         TCGA-C5-A7X3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DR-A0ZM         TCGA-DS-A0VK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A0VN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A3LQ         TCGA-DS-A7WF         TCGA-DS-A7WH 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DS-A7WI         TCGA-EA-A1QS         TCGA-EA-A1QT 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EA-A3QD         TCGA-EA-A3QE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A410         TCGA-EA-A411         TCGA-EA-A43B 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A44S         TCGA-EA-A4BA         TCGA-EA-A50E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A556         TCGA-EA-A5O9         TCGA-EA-A5ZE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EA-A5ZF         TCGA-EK-A2R7         TCGA-EK-A3GK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A1H6         TCGA-EX-A3L1 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-EX-A69L         TCGA-EX-A69M         TCGA-FU-A2QG 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3WB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-FU-A57G         TCGA-FU-A770 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK         TCGA-HM-A4S6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HM-A6W2         TCGA-IR-A3L7         TCGA-IR-A3LA 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LB         TCGA-IR-A3LC         TCGA-IR-A3LF 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IR-A3LH         TCGA-IR-A3LI         TCGA-IR-A3LK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A5VG         TCGA-JW-A5VI         TCGA-JW-A5VJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-JW-A5VK         TCGA-JW-A69B         TCGA-LP-A5U3 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-PN-A8MA         TCGA-Q1-A5R1         TCGA-Q1-A5R2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Q1-A5R3         TCGA-Q1-A6DV         TCGA-Q1-A73P 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D77V37, continuous
D77V38, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  1
  20Q LOSS WILD-TYPE 72 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    1
  20Q LOSS WILD-TYPE   72   13
         clus
vv        20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ABSENT                 1                 72
  PRESENT                1                 13
[1] 2 2
[1] FALSE
D77V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  20Q LOSS MUTATED     0    0   1    0    1  0   0    1    0   0   0  0  0
  20Q LOSS WILD-TYPE   2    1  21   51   20  3   6    5    8  13   2  1  7
D77V40, multiclass
      clus
vv     20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 1                 21
  T1B1                0                 51
  T1B2                1                 20
  T2                  0                  3
  T2A                 0                  6
  T2A1                1                  5
  T2A2                0                  8
  T2B                 0                 13
  T3B                 0                  2
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V41, continuous

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    20   5
  21Q LOSS WILD-TYPE 117  27
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                25                144 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 5                 27 
$`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-DR-A0ZL TCGA-DS-A0VL TCGA-EA-A3HR TCGA-EA-A411 
       73.45         9.34        87.75         2.66         1.32         1.35 
TCGA-EA-A439 TCGA-EA-A556 TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2RJ TCGA-EK-A2RL 
       14.50        14.89        12.59         0.53         1.18        23.70 
TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3NI TCGA-HM-A3JJ TCGA-HM-A6W2 TCGA-JW-A5VG 
        6.94        23.84         1.45        21.67         4.11        14.43 
TCGA-PN-A8MA 
        2.96 

$`21Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ TCGA-C5-A1BK 
       49.48        68.84        18.74        36.56       144.16       177.04 
TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M6 
      173.29        82.85         5.46        19.86        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M8 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       46.32        30.21        57.73        53.16        38.99        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LX TCGA-C5-A2LY 
        2.43        40.93         3.58        44.22        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         0.82        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       182.93        25.35       101.82       134.33        15.48 
TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH TCGA-C5-A7UI 
        9.67        73.41        17.19        85.55        60.69        94.95 
TCGA-C5-A7X5 TCGA-C5-A7X8 TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       13.61         2.73        58.88        36.76       117.99       118.65 
TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI TCGA-EA-A1QS 
       22.98        16.83        16.18         7.33         8.28         0.76 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
       12.36         1.74         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A44S TCGA-EA-A4BA TCGA-EA-A50E 
       14.50         1.35         1.81        12.66        12.82         0.26 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2R7 TCGA-EK-A2RB TCGA-EK-A2RC 
       13.48        45.96         6.64         0.59         0.07         4.04 
TCGA-EK-A2RD TCGA-EK-A2RE TCGA-EK-A2RM TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GJ 
        0.03         0.36         2.24         0.10         0.07         0.10 
TCGA-EK-A3GK TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.03        20.35         7.92        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.12         1.22         0.92         2.17         0.66         1.02 
TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G 
        1.58         1.48         0.82         3.52         1.35         1.32 
TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-IR-A3L7 
        1.97         1.12        25.41        20.78        14.93       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       26.56        36.36        16.64        19.33        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       10.06         5.13         0.10         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW 
        3.72         3.45         5.85         3.39         3.72         5.75 
TCGA-Q1-A73P TCGA-Q1-A73R TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
        4.80         6.25        19.59         3.88        11.67        93.99 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.46               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             87.75             182.93 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            12.590             13.595 
[1] "0.5 - 87.8 (12.6)"  "0.0 - 182.9 (13.6)"
[1] "hr=" "1.5"
D78V2, continuous
                    vv
clus                 T1 T2+T3+T4
  21Q LOSS MUTATED   14        8
  21Q LOSS WILD-TYPE 83       31
D78V3, multiclass
          clus
vv         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                     14                 83
  T2+T3+T4                8                 31
[1] 2 2
[1] FALSE
D78V4, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   15  6
  21Q LOSS WILD-TYPE 72 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     15    6
  21Q LOSS WILD-TYPE   72   34
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               15                 72
  1                6                 34
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED   12  1  9
  21Q LOSS WILD-TYPE 60  2 56
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               12                 60
  M1                1                  2
  MX                9                 56
[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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED               1                               21
  21Q LOSS WILD-TYPE             1                              123
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  21Q LOSS MUTATED                                               0
  21Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  21Q LOSS MUTATED                                     3
  21Q LOSS WILD-TYPE                                  17
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  21Q LOSS MUTATED                                           1
  21Q LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  21Q LOSS MUTATED                                              0
  21Q LOSS WILD-TYPE                                            4
D78V6, multiclass
                                               clus
vv                                              21Q LOSS MUTATED
  ADENOSQUAMOUS                                                1
  CERVICAL SQUAMOUS CELL CARCINOMA                            21
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          3
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 0
                                               clus
vv                                              21Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  1
  CERVICAL SQUAMOUS CELL CARCINOMA                             123
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           17
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   4
[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"
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4  22
  21Q LOSS WILD-TYPE  23 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   22
  21Q LOSS WILD-TYPE   23  127
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                 23
  YES               22                127
[1] 2 2
[1] FALSE
D78V8, continuous
D78V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     2
  21Q LOSS WILD-TYPE                                6    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED                           8
  21Q LOSS WILD-TYPE                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           0    15
  21Q LOSS WILD-TYPE                                         1   115
D78V10, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  6
  ASIAN                                                    2                 13
  BLACK OR AFRICAN AMERICAN                                8                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                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"
D78V11, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  21
  21Q LOSS WILD-TYPE  10 106
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   21
  21Q LOSS WILD-TYPE   10  106
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 10
  NOT HISPANIC OR LATINO               21                106
[1] 2 2
[1] FALSE
D78V12, continuous
D78V13, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    9  3
  21Q LOSS WILD-TYPE 39 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      9    3
  21Q LOSS WILD-TYPE   39   16
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  TUMOR FREE                9                 39
  WITH TUMOR                3                 16
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  21Q LOSS MUTATED         1      3       0            21       1
  21Q LOSS WILD-TYPE       0      7       6           126      11
D78V14, multiclass
               clus
vv              21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NIGERIA                      1                  0
  RUSSIA                       3                  7
  UKRAINE                      0                  6
  UNITED STATES               21                126
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  21Q LOSS MUTATED    0  8 18  0  0
  21Q LOSS WILD-TYPE 14 75 54  1  5
D78V15, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  G1                0                 14
  G2                8                 75
  G3               18                 54
  G4                0                  1
  GX                0                  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"
D78V16, continuous
D78V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  21Q LOSS MUTATED                                             0
  21Q LOSS WILD-TYPE                                          21
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  21Q LOSS MUTATED                                        0
  21Q LOSS WILD-TYPE                                      8
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  21Q LOSS MUTATED                                                 0
  21Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  21Q LOSS MUTATED                6                  12
  21Q LOSS WILD-TYPE             30                  71
D78V18, multiclass
                                                 clus
vv                                                21Q LOSS MUTATED
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    0
  CURRENT REFORMED SMOKER FOR > 15 YEARS                         0
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                0
  CURRENT SMOKER                                                 6
  LIFELONG NON-SMOKER                                           12
                                                 clus
vv                                                21Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     21
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           8
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  30
  LIFELONG NON-SMOKER                                             71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  21Q LOSS MUTATED             0        6             4        0
  21Q LOSS WILD-TYPE          17       31             7        5
D78V20, multiclass
               clus
vv              21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COMBINATION                  0                 17
  EXTERNAL                     6                 31
  EXTERNAL BEAM                4                  7
  INTERNAL                     0                  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"
D78V21, binary
                    cls
clus                 0 1
  21Q LOSS MUTATED   5 0
  21Q LOSS WILD-TYPE 6 3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5    0
  21Q LOSS WILD-TYPE    6    3
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CGY                5                  6
  GY                 0                  3
[1] 2 2
[1] FALSE
D78V22, continuous
D78V23, continuous
D78V24, continuous
D78V25, continuous
D78V26, continuous
D78V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  21Q LOSS MUTATED                                     0
  21Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  21Q LOSS MUTATED                                     2
  21Q LOSS WILD-TYPE                                   4
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  21Q LOSS MUTATED                         1                       0
  21Q LOSS WILD-TYPE                       8                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  21Q LOSS MUTATED                         0
  21Q LOSS WILD-TYPE                       5
D78V28, multiclass
                                     clus
vv                                    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                2                  4
  OTHER LOCATION, SPECIFY                            1                  8
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            0                  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)
  21Q LOSS MUTATED                                               0
  21Q LOSS WILD-TYPE                                             2
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  21Q LOSS MUTATED                                                0
  21Q LOSS WILD-TYPE                                             10
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  21Q LOSS MUTATED                                                                                   7
  21Q LOSS WILD-TYPE                                                                                47
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  21Q LOSS MUTATED                                                                                             14
  21Q LOSS WILD-TYPE                                                                                           63
D78V29, multiclass
                                                                                              clus
vv                                                                                             21Q 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)                           7
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)               14
                                                                                              clus
vv                                                                                             21Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 2
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                               10
  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)                 63
[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"
D78V30, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    9 10
  21Q LOSS WILD-TYPE 45 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      9   10
  21Q LOSS WILD-TYPE   45   49
         clus
vv        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ABSENT                 9                 45
  PRESENT               10                 49
[1] 2 2
[1] FALSE
D78V31, continuous
D78V32, continuous
D78V33, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    3 16
  21Q LOSS WILD-TYPE 32 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3   16
  21Q LOSS WILD-TYPE   32   65
                                          clus
vv                                         21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    3                 32
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               16                 65
[1] 2 2
[1] FALSE
D78V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  21Q LOSS MUTATED       0                   20                   0
  21Q LOSS WILD-TYPE     3                   93                   5
D78V35, multiclass
                      clus
vv                     21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  OTHER                               0                  3
  RADICAL HYSTERECTOMY               20                 93
  SIMPLE HYSTERECTOMY                 0                  5
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  21Q LOSS MUTATED              2           5          7
  21Q LOSS WILD-TYPE            6          35         33
D78V36, multiclass
              clus
vv             21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CURRENT USER                2                  6
  FORMER USER                 5                 35
  NEVER USED                  7                 33
[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, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   11  4
  21Q LOSS WILD-TYPE 62 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     11    4
  21Q LOSS WILD-TYPE   62   10
         clus
vv        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ABSENT                11                 62
  PRESENT                4                 10
[1] 2 2
[1] FALSE
D78V39, continuous
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  21Q LOSS MUTATED     0    0   3   10    1  0   3    3    0   1   1  0  0
  21Q LOSS WILD-TYPE   2    1  19   41   20  3   3    3    8  12   1  1  7
D78V40, multiclass
      clus
vv     21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 3                 19
  T1B1               10                 41
  T1B2                1                 20
  T2                  0                  3
  T2A                 3                  3
  T2A1                3                  3
  T2A2                0                  8
  T2B                 1                 12
  T3B                 1                  1
  T4                  0                  1
  TX                  0                  7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V41, continuous

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    27   8
  22Q LOSS WILD-TYPE 110  24
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                35                134 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 24 
$`22Q LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A1BF TCGA-C5-A1BL TCGA-C5-A1BN TCGA-C5-A1M6 TCGA-C5-A1M8 
       23.67        18.74       173.29         5.46        31.40        30.21 
TCGA-C5-A1ME TCGA-C5-A1MJ TCGA-C5-A2LT TCGA-C5-A2LX TCGA-C5-A3HD TCGA-C5-A3HE 
       57.73         0.46        73.18        83.05        52.01        18.02 
TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A411 
        9.34         2.73       118.65        12.36         1.32         1.35 
TCGA-EA-A439 TCGA-EA-A44S TCGA-EK-A2GZ TCGA-EK-A2PG TCGA-EK-A2R7 TCGA-EK-A2RJ 
       14.50        12.66        12.59         0.53         0.59         1.18 
TCGA-EK-A2RN TCGA-HM-A3JJ TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-JW-A5VG 
        0.10        21.67       137.16        66.81       117.40        14.43 
TCGA-Q1-A5R1 TCGA-Q1-A5R2 TCGA-Q1-A6DT TCGA-R2-A69V TCGA-UC-A7PD 
        3.72         3.45         3.39        19.59        11.67 

$`22Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A0TN TCGA-C5-A1BE TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        57.04        11.44        68.84        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BM TCGA-C5-A1BQ TCGA-C5-A1M5 TCGA-C5-A1M7 TCGA-C5-A1M9 
      177.04        82.85        19.86        67.46        46.32        35.01 
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-A2LV TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 
       44.22        73.45        78.35       100.14        38.43         0.82 
TCGA-C5-A3HF TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CJ TCGA-C5-A7CK 
       17.85        20.42       182.93        25.35       101.82       134.33 
TCGA-C5-A7CL TCGA-C5-A7CM TCGA-C5-A7CO TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UH 
       15.48         9.67        73.41        17.19        85.55        60.69 
TCGA-C5-A7UI TCGA-C5-A7X5 TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       94.95        13.61        87.75        58.88        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WF TCGA-DS-A7WH TCGA-DS-A7WI 
      117.99        22.98        16.83        16.18         7.33         8.28 
TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A3QD TCGA-EA-A3QE 
        0.76         1.74         0.82         0.62        13.05         1.18 
TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A43B TCGA-EA-A4BA TCGA-EA-A50E TCGA-EA-A556 
       14.50         1.35         1.81        12.82         0.26        14.89 
TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZE TCGA-EA-A5ZF TCGA-EA-A6QX 
        1.48        13.91         0.69        14.99        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD 
       13.48        45.96         6.64         0.07         4.04         0.03 
TCGA-EK-A2RE TCGA-EK-A2RL TCGA-EK-A2RM TCGA-EK-A2RO TCGA-EK-A3GJ TCGA-EK-A3GK 
        0.36        23.70         2.24         0.07         0.10         0.10 
TCGA-EK-A3GN TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.03        20.35         7.92         6.94        14.70         4.47 
TCGA-EX-A69M TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.12         1.22        23.84         0.92         2.17         0.66 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ 
        1.02         1.45         1.58         1.48         0.82         3.52 
TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A5XV TCGA-FU-A770 TCGA-HG-A2PA TCGA-HM-A3JK 
        1.35         1.32         1.97         1.12        25.41        20.78 
TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
       14.93         4.11       147.39        96.95        78.71        81.96 
TCGA-IR-A3LK TCGA-IR-A3LL TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A5VL 
       26.56        36.36        16.64        19.33        20.48        15.58 
TCGA-JW-A69B TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AW TCGA-LP-A4AX TCGA-LP-A5U3 
       10.06         5.13         0.10         0.89         0.07         0.82 
TCGA-MU-A51Y TCGA-MU-A5YI TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-MY-A5BF 
       13.87         0.03         5.42        29.72         0.07         4.34 
TCGA-PN-A8MA TCGA-Q1-A5R3 TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        2.96         5.85         3.72         5.75         4.80         6.25 
TCGA-RA-A741 TCGA-UC-A7PF 
        3.88        93.99 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.10               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            173.29             182.93 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             14.43              13.53 
[1] "0.1 - 173.3 (14.4)" "0.0 - 182.9 (13.5)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 T1 T2+T3+T4
  22Q LOSS MUTATED   19        7
  22Q LOSS WILD-TYPE 78       32
D79V3, multiclass
          clus
vv         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                     19                 78
  T2+T3+T4                7                 32
[1] 2 2
[1] FALSE
D79V4, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   19  7
  22Q LOSS WILD-TYPE 68 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     19    7
  22Q LOSS WILD-TYPE   68   33
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               19                 68
  1                7                 33
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   18  0 11
  22Q LOSS WILD-TYPE 54  3 54
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               18                 54
  M1                0                  3
  MX               11                 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"
                    vv
clus                 ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED               0                               30
  22Q LOSS WILD-TYPE             2                              114
                    vv
clus                 ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  22Q LOSS MUTATED                                               0
  22Q LOSS WILD-TYPE                                             4
                    vv
clus                 ENDOCERVICAL TYPE OF ADENOCARCINOMA
  22Q LOSS MUTATED                                     4
  22Q LOSS WILD-TYPE                                  16
                    vv
clus                 ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  22Q LOSS MUTATED                                           1
  22Q LOSS WILD-TYPE                                         1
                    vv
clus                 MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  22Q LOSS MUTATED                                              2
  22Q LOSS WILD-TYPE                                            2
D79V6, multiclass
                                               clus
vv                                              22Q LOSS MUTATED
  ADENOSQUAMOUS                                                0
  CERVICAL SQUAMOUS CELL CARCINOMA                            30
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          4
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                    1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                 2
                                               clus
vv                                              22Q LOSS WILD-TYPE
  ADENOSQUAMOUS                                                  2
  CERVICAL SQUAMOUS CELL CARCINOMA                             114
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                  4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                           16
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                      1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                   2
[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"
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     9  28
  22Q LOSS WILD-TYPE  18 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   28
  22Q LOSS WILD-TYPE   18  121
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 9                 18
  YES               28                121
[1] 2 2
[1] FALSE
D79V8, continuous
D79V9, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  2     1
  22Q LOSS WILD-TYPE                                5    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED                           3
  22Q LOSS WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           0    31
  22Q LOSS WILD-TYPE                                         1    99
D79V10, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  5
  ASIAN                                                    1                 14
  BLACK OR AFRICAN AMERICAN                                3                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   31                 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"
D79V11, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     2  27
  22Q LOSS WILD-TYPE   9 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   27
  22Q LOSS WILD-TYPE    9  100
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  9
  NOT HISPANIC OR LATINO               27                100
[1] 2 2
[1] FALSE
D79V12, continuous
D79V13, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   13  4
  22Q LOSS WILD-TYPE 35 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     13    4
  22Q LOSS WILD-TYPE   35   15
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  TUMOR FREE               13                 35
  WITH TUMOR                4                 15
[1] 2 2
[1] FALSE
                    vv
clus                 NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  22Q LOSS MUTATED         0      3       1            32       1
  22Q LOSS WILD-TYPE       1      7       5           115      11
D79V14, multiclass
               clus
vv              22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NIGERIA                      0                  1
  RUSSIA                       3                  7
  UKRAINE                      1                  5
  UNITED STATES               32                115
  VIETNAM                      1                 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"
                    vv
clus                 G1 G2 G3 G4 GX
  22Q LOSS MUTATED    2 17 17  0  1
  22Q LOSS WILD-TYPE 12 66 55  1  4
D79V15, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  G1                2                 12
  G2               17                 66
  G3               17                 55
  G4                0                  1
  GX                1                  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"
D79V16, continuous
D79V17, continuous
                    vv
clus                 CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  22Q LOSS MUTATED                                             3
  22Q LOSS WILD-TYPE                                          18
                    vv
clus                 CURRENT REFORMED SMOKER FOR > 15 YEARS
  22Q LOSS MUTATED                                        1
  22Q LOSS WILD-TYPE                                      7
                    vv
clus                 CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  22Q LOSS MUTATED                                                 0
  22Q LOSS WILD-TYPE                                               1
                    vv
clus                 CURRENT SMOKER LIFELONG NON-SMOKER
  22Q LOSS MUTATED                6                  19
  22Q LOSS WILD-TYPE             30                  64
D79V18, multiclass
                                                 clus
vv                                                22Q 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                                                 6
  LIFELONG NON-SMOKER                                           19
                                                 clus
vv                                                22Q LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                     18
  CURRENT REFORMED SMOKER FOR > 15 YEARS                           7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                  1
  CURRENT SMOKER                                                  30
  LIFELONG NON-SMOKER                                             64
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V19, continuous
                    vv
clus                 COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  22Q LOSS MUTATED             5       10             4        1
  22Q LOSS WILD-TYPE          12       27             7        4
D79V20, multiclass
               clus
vv              22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COMBINATION                  5                 12
  EXTERNAL                    10                 27
  EXTERNAL BEAM                4                  7
  INTERNAL                     1                  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"
D79V21, binary
                    cls
clus                 0 1
  22Q LOSS MUTATED   2 1
  22Q LOSS WILD-TYPE 9 2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2    1
  22Q LOSS WILD-TYPE    9    2
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CGY                2                  9
  GY                 1                  2
[1] 2 2
[1] FALSE
D79V22, continuous
D79V23, continuous
D79V24, continuous
D79V25, continuous
D79V26, continuous
D79V27, continuous
                    vv
clus                 MACROSCOPIC PARAMETRIAL INVOLVEMENT
  22Q LOSS MUTATED                                     0
  22Q LOSS WILD-TYPE                                   2
                    vv
clus                 MICROSCOPIC PARAMETRIAL INVOLVEMENT
  22Q LOSS MUTATED                                     1
  22Q LOSS WILD-TYPE                                   5
                    vv
clus                 OTHER LOCATION, SPECIFY POSITIVE BLADDER MARGIN
  22Q LOSS MUTATED                         3                       0
  22Q LOSS WILD-TYPE                       6                       1
                    vv
clus                 POSITIVE VAGINAL MARGIN
  22Q LOSS MUTATED                         1
  22Q LOSS WILD-TYPE                       4
D79V28, multiclass
                                     clus
vv                                    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT                0                  2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT                1                  5
  OTHER LOCATION, SPECIFY                            3                  6
  POSITIVE BLADDER MARGIN                            0                  1
  POSITIVE VAGINAL MARGIN                            1                  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)
  22Q LOSS MUTATED                                               1
  22Q LOSS WILD-TYPE                                             1
                    vv
clus                 PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  22Q LOSS MUTATED                                                1
  22Q LOSS WILD-TYPE                                              9
                    vv
clus                 POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  22Q LOSS MUTATED                                                                                  14
  22Q LOSS WILD-TYPE                                                                                40
                    vv
clus                 PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  22Q LOSS MUTATED                                                                                             13
  22Q LOSS WILD-TYPE                                                                                           64
D79V29, multiclass
                                                                                              clus
vv                                                                                             22Q LOSS MUTATED
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                               1
  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)               13
                                                                                              clus
vv                                                                                             22Q LOSS WILD-TYPE
  INDETERMINATE (NEITHER PRE OR POSTMENOPAUSAL)                                                                 1
  PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)                                                                9
  POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)                            40
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                 64
[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"
D79V30, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    9 17
  22Q LOSS WILD-TYPE 45 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      9   17
  22Q LOSS WILD-TYPE   45   42
         clus
vv        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ABSENT                 9                 45
  PRESENT               17                 42
[1] 2 2
[1] FALSE
D79V31, continuous
D79V32, continuous
D79V33, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    6 18
  22Q LOSS WILD-TYPE 29 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   18
  22Q LOSS WILD-TYPE   29   63
                                          clus
vv                                         22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                    6                 29
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA               18                 63
[1] 2 2
[1] FALSE
D79V34, continuous
                    vv
clus                 OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  22Q LOSS MUTATED       1                   23                   1
  22Q LOSS WILD-TYPE     2                   90                   4
D79V35, multiclass
                      clus
vv                     22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  OTHER                               1                  2
  RADICAL HYSTERECTOMY               23                 90
  SIMPLE HYSTERECTOMY                 1                  4
[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"
                    vv
clus                 CURRENT USER FORMER USER NEVER USED
  22Q LOSS MUTATED              4           9         10
  22Q LOSS WILD-TYPE            4          31         30
D79V36, multiclass
              clus
vv             22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CURRENT USER                4                  4
  FORMER USER                 9                 31
  NEVER USED                 10                 30
[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, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   17  2
  22Q LOSS WILD-TYPE 56 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     17    2
  22Q LOSS WILD-TYPE   56   12
         clus
vv        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ABSENT                17                 56
  PRESENT                2                 12
[1] 2 2
[1] FALSE
D79V39, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  8 
        TCGA-C5-A1MH         TCGA-C5-A1MN         TCGA-C5-A1MP 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EK-A2RO         TCGA-HM-A3JK         TCGA-JW-A852 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-MU-A51Y         TCGA-MU-A8JM 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
                    vv
clus                 T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  22Q LOSS MUTATED     0    0   6   10    3  1   3    1    1   1   0  0  3
  22Q LOSS WILD-TYPE   2    1  16   41   18  2   3    5    7  12   2  1  4
D79V40, multiclass
      clus
vv     22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1A                 0                  2
  T1A1                0                  1
  T1B                 6                 16
  T1B1               10                 41
  T1B2                3                 18
  T2                  1                  2
  T2A                 3                  3
  T2A1                1                  5
  T2A2                1                  7
  T2B                 1                 12
  T3B                 0                  2
  T4                  0                  1
  TX                  3                  4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V41, continuous

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    23  10
  XQ LOSS WILD-TYPE 114  22
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               33               136 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               10                22 
$`XQ LOSS MUTATED`
TCGA-BI-A20A TCGA-C5-A0TN TCGA-C5-A1BQ TCGA-C5-A1M8 TCGA-C5-A1MK TCGA-C5-A1MN 
       23.67        11.44        19.86        30.21         2.43        40.93 
TCGA-C5-A3HD TCGA-C5-A7CJ TCGA-C5-A7CO TCGA-C5-A7UH TCGA-C5-A7X5 TCGA-DS-A0VK 
       52.01       101.82        73.41        60.69        13.61        36.76 
TCGA-DS-A0VN TCGA-DS-A7WF TCGA-EA-A1QT TCGA-EA-A3QE TCGA-EA-A43B TCGA-EA-A44S 
      118.65        16.18        12.36         1.18         1.81        12.66 
TCGA-EA-A556 TCGA-EA-A5ZE TCGA-EK-A2RE TCGA-EK-A3GJ TCGA-EK-A3GK TCGA-EX-A1H5 
       14.89        14.99         0.36         0.10         0.10        20.35 
TCGA-EX-A1H6 TCGA-EX-A69M TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A5XV TCGA-IR-A3LK 
        7.92         6.12         0.92         0.66         1.97        26.56 
TCGA-JW-A5VL TCGA-LP-A4AW TCGA-MY-A5BF 
       15.58         0.89         4.34 

$`XQ LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BE TCGA-C5-A1BF TCGA-C5-A1BI TCGA-C5-A1BJ 
       49.48        57.04        68.84        18.74        36.56       144.16 
TCGA-C5-A1BK TCGA-C5-A1BL TCGA-C5-A1BM TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1M6 
      177.04       173.29        82.85         5.46        67.46        31.40 
TCGA-C5-A1M7 TCGA-C5-A1M9 TCGA-C5-A1ME TCGA-C5-A1MF TCGA-C5-A1MH TCGA-C5-A1MI 
       46.32        35.01        57.73        53.16        38.99        35.61 
TCGA-C5-A1MJ TCGA-C5-A1MP TCGA-C5-A2LS TCGA-C5-A2LT TCGA-C5-A2LV TCGA-C5-A2LX 
        0.46         3.58        44.22        73.18        73.45        83.05 
TCGA-C5-A2LY TCGA-C5-A2LZ TCGA-C5-A2M1 TCGA-C5-A2M2 TCGA-C5-A3HE TCGA-C5-A3HF 
       78.35       100.14        38.43         0.82        18.02        17.85 
TCGA-C5-A3HL TCGA-C5-A7CG TCGA-C5-A7CH TCGA-C5-A7CK TCGA-C5-A7CL TCGA-C5-A7CM 
       20.42       182.93        25.35       134.33        15.48         9.67 
TCGA-C5-A7UC TCGA-C5-A7UE TCGA-C5-A7UI TCGA-C5-A7X3 TCGA-C5-A7X8 TCGA-DR-A0ZL 
       17.19        85.55        94.95         9.34         2.73        87.75 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-DS-A5RQ TCGA-DS-A7WH 
       58.88         2.66       117.99        22.98        16.83         7.33 
TCGA-DS-A7WI TCGA-EA-A1QS TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        8.28         0.76         1.74         1.32         0.82         0.62 
TCGA-EA-A3QD TCGA-EA-A3Y4 TCGA-EA-A410 TCGA-EA-A411 TCGA-EA-A439 TCGA-EA-A4BA 
       13.05        14.50         1.35         1.35        14.50        12.82 
TCGA-EA-A50E TCGA-EA-A5FO TCGA-EA-A5O9 TCGA-EA-A5ZD TCGA-EA-A5ZF TCGA-EA-A6QX 
        0.26         1.48        13.91         0.69        14.96        13.58 
TCGA-EA-A78R TCGA-EK-A2GZ TCGA-EK-A2H0 TCGA-EK-A2IP TCGA-EK-A2PG TCGA-EK-A2R7 
       13.48        12.59        45.96         6.64         0.53         0.59 
TCGA-EK-A2RB TCGA-EK-A2RC TCGA-EK-A2RD TCGA-EK-A2RJ TCGA-EK-A2RL TCGA-EK-A2RM 
        0.07         4.04         0.03         1.18        23.70         2.24 
TCGA-EK-A2RN TCGA-EK-A2RO TCGA-EK-A3GN TCGA-EX-A3L1 TCGA-EX-A449 TCGA-EX-A69L 
        0.10         0.07         0.03         6.94        14.70         4.47 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ 
        1.22        23.84         2.17         1.02         1.45         1.58 
TCGA-FU-A3TX TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-FU-A40J TCGA-FU-A57G TCGA-FU-A770 
        1.48         0.82         3.52         1.35         1.32         1.12 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK TCGA-HM-A4S6 TCGA-HM-A6W2 TCGA-IR-A3L7 
       25.41        21.67        20.78        14.93         4.11       147.39 
TCGA-IR-A3LA TCGA-IR-A3LB TCGA-IR-A3LC TCGA-IR-A3LF TCGA-IR-A3LH TCGA-IR-A3LI 
      137.16        66.81       117.40        96.95        78.71        81.96 
TCGA-IR-A3LL TCGA-JW-A5VG TCGA-JW-A5VI TCGA-JW-A5VJ TCGA-JW-A5VK TCGA-JW-A69B 
       36.36        14.43        16.64        19.33        20.48        10.06 
TCGA-JW-A852 TCGA-LP-A4AU TCGA-LP-A4AX TCGA-LP-A5U3 TCGA-MU-A51Y TCGA-MU-A5YI 
        5.13         0.10         0.07         0.82        13.87         0.03 
TCGA-MU-A8JM TCGA-MY-A5BD TCGA-MY-A5BE TCGA-PN-A8MA TCGA-Q1-A5R1 TCGA-Q1-A5R2 
        5.42        29.72         0.07         2.96         3.72         3.45 
TCGA-Q1-A5R3 TCGA-Q1-A6DT TCGA-Q1-A6DV TCGA-Q1-A6DW TCGA-Q1-A73P TCGA-Q1-A73R 
        5.85         3.39         3.72         5.75         4.80         6.25 
TCGA-R2-A69V TCGA-RA-A741 TCGA-UC-A7PD TCGA-UC-A7PF 
       19.59         3.88        11.67        93.99 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.10              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           118.65            182.93 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            13.61             13.53 
[1] "0.1 - 118.7 (13.6)" "0.0 - 182.9 (13.5)"
[1] "hr=" "2.3"
D80V2, continuous
                   vv
clus                T1 T2+T3+T4
  XQ LOSS MUTATED   22        5
  XQ LOSS WILD-TYPE 75       34
D80V3, multiclass
          clus
vv         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                    22                75
  T2+T3+T4               5                34
[1] 2 2
[1] FALSE
D80V4, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   19  7
  XQ LOSS WILD-TYPE 68 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     19    7
  XQ LOSS WILD-TYPE   68   33
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              19                68
  1               7                33
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  XQ LOSS MUTATED   12  0 13
  XQ LOSS WILD-TYPE 60  3 52
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              12                60
  M1               0                 3
  MX              13                52
[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"
                   vv
clus                ADENOSQUAMOUS CERVICAL SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED               1                               31
  XQ LOSS WILD-TYPE             1                              113
                   vv
clus                ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE
  XQ LOSS MUTATED                                               0
  XQ LOSS WILD-TYPE                                             4
                   vv
clus                ENDOCERVICAL TYPE OF ADENOCARCINOMA
  XQ LOSS MUTATED                                     2
  XQ LOSS WILD-TYPE                                  18
                   vv
clus                ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX
  XQ LOSS MUTATED                                           1
  XQ LOSS WILD-TYPE                                         1
                   vv
clus                MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE
  XQ LOSS MUTATED                                              0
  XQ LOSS WILD-TYPE                                            4
D80V6, multiclass
                                               clus
vv                                              XQ LOSS MUTATED
  ADENOSQUAMOUS                                               1
  CERVICAL SQUAMOUS CELL CARCINOMA                           31
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE               0
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                         2
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                   1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                0
                                               clus
vv                                              XQ LOSS WILD-TYPE
  ADENOSQUAMOUS                                                 1
  CERVICAL SQUAMOUS CELL CARCINOMA                            113
  ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE                 4
  ENDOCERVICAL TYPE OF ADENOCARCINOMA                          18
  ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX                     1
  MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE                  4
[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"
D80V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     6  29
  XQ LOSS WILD-TYPE  21 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      6   29
  XQ LOSS WILD-TYPE   21  120
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                6                21
  YES              29               120
[1] 2 2
[1] FALSE
D80V8, continuous
D80V9, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  1     2
  XQ LOSS WILD-TYPE                                6    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED                           3
  XQ LOSS WILD-TYPE                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           1    27
  XQ LOSS WILD-TYPE                                         0   103
D80V10, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 6
  ASIAN                                                   2                13
  BLACK OR AFRICAN AMERICAN                               3                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  27               103
[1] 5 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
  XQ LOSS MUTATED    2 28
  XQ LOSS WILD-TYPE  9 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   28
  XQ LOSS WILD-TYPE    9   99
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 9
  NOT HISPANIC OR LATINO              28                99
[1] 2 2
[1] FALSE
D80V12, continuous
D80V13, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   12  4
  XQ LOSS WILD-TYPE 36 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     12    4
  XQ LOSS WILD-TYPE   36   15
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  TUMOR FREE              12                36
  WITH TUMOR               4                15
[1] 2 2
[1] FALSE
                   vv
clus                NIGERIA RUSSIA UKRAINE UNITED STATES VIETNAM
  XQ LOSS MUTATED         0      3       2            28       2
  XQ LOSS WILD-TYPE       1      7       4           119      10
D80V14, multiclass
               clus
vv              XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NIGERIA                     0                 1
  RUSSIA                      3                 7
  UKRAINE                     2                 4
  UNITED STATES              28               119
  VIETNAM                     2                10
[1] 5 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                G1 G2 G3 G4 GX
  XQ LOSS MUTATED    4 14 16  0  0
  XQ LOSS WILD-TYPE 10 69 56  1  5
D80V15, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  G1               4                10
  G2              14                69
  G3              16                56
  G4               0                 1
  GX               0                 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"
D80V16, continuous
D80V17, continuous
                   vv
clus                CURRENT REFORMED SMOKER FOR < OR = 15 YEARS
  XQ LOSS MUTATED                                             5
  XQ LOSS WILD-TYPE                                          16
                   vv
clus                CURRENT REFORMED SMOKER FOR > 15 YEARS
  XQ LOSS MUTATED                                        1
  XQ LOSS WILD-TYPE                                      7
                   vv
clus                CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED
  XQ LOSS MUTATED                                                 0
  XQ LOSS WILD-TYPE                                               1
                   vv
clus                CURRENT SMOKER LIFELONG NON-SMOKER
  XQ LOSS MUTATED                7                  15
  XQ LOSS WILD-TYPE             29                  68
D80V18, multiclass
                                                 clus
vv                                                XQ 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                                                7
  LIFELONG NON-SMOKER                                          15
                                                 clus
vv                                                XQ LOSS WILD-TYPE
  CURRENT REFORMED SMOKER FOR < OR = 15 YEARS                    16
  CURRENT REFORMED SMOKER FOR > 15 YEARS                          7
  CURRENT REFORMED SMOKER, DURATION NOT SPECIFIED                 1
  CURRENT SMOKER                                                 29
  LIFELONG NON-SMOKER                                            68
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V19, continuous
                   vv
clus                COMBINATION EXTERNAL EXTERNAL BEAM INTERNAL
  XQ LOSS MUTATED             2        4             4        2
  XQ LOSS WILD-TYPE          15       33             7        3
D80V20, multiclass
               clus
vv              XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COMBINATION                 2                15
  EXTERNAL                    4                33
  EXTERNAL BEAM               4                 7
  INTERNAL                    2                 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"
D80V21, binary
                   cls
clus                0 1
  XQ LOSS MUTATED   3 0
  XQ LOSS WILD-TYPE 8 3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    0
  XQ LOSS WILD-TYPE    8    3
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CGY               3                 8
  GY                0                 3
[1] 2 2
[1] FALSE
D80V22, continuous
D80V23, continuous
D80V24, continuous
D80V25, continuous
D80V26, continuous
D80V27, continuous
                   vv
clus                MACROSCOPIC PARAMETRIAL INVOLVEMENT
  XQ LOSS MUTATED                                     0
  XQ LOSS WILD-TYPE                                   2
                   vv
clus                MICROSCOPIC PARAMETRIAL INVOLVEMENT OTHER LOCATION, SPECIFY
  XQ LOSS MUTATED                                     4                       1
  XQ LOSS WILD-TYPE                                   2                       8
                   vv
clus                POSITIVE BLADDER MARGIN POSITIVE VAGINAL MARGIN
  XQ LOSS MUTATED                         0                       1
  XQ LOSS WILD-TYPE                       1                       4
D80V28, multiclass
                                     clus
vv                                    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  MACROSCOPIC PARAMETRIAL INVOLVEMENT               0                 2
  MICROSCOPIC PARAMETRIAL INVOLVEMENT               4                 2
  OTHER LOCATION, SPECIFY                           1                 8
  POSITIVE BLADDER MARGIN                           0                 1
  POSITIVE VAGINAL MARGIN                           1                 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)
  XQ LOSS MUTATED                                               1
  XQ LOSS WILD-TYPE                                             1
                   vv
clus                PERI (6-12 MONTHS SINCE LAST MENSTRUAL PERIOD)
  XQ LOSS MUTATED                                                3
  XQ LOSS WILD-TYPE                                              7
                   vv
clus                POST (PRIOR BILATERAL OVARIECTOMY OR >12 MO SINCE LMP WITH NO PRIOR HYSTERECTOMY)
  XQ LOSS MUTATED                                                                                   9
  XQ LOSS WILD-TYPE                                                                                45
                   vv
clus                PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)
  XQ LOSS MUTATED                                                                                             14
  XQ LOSS WILD-TYPE                                                                                           63
D80V29, multiclass
                                                                                              clus
vv                                                                                             XQ 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)                          9
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)              14
                                                                                              clus
vv                                                                                             XQ LOSS WILD-TYPE
  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)                           45
  PRE (<6 MONTHS SINCE LMP AND NO PRIOR BILATERAL OVARIECTOMY AND NOT ON ESTROGEN REPLACEMENT)                63
[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"
D80V30, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    9 11
  XQ LOSS WILD-TYPE 45 48
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      9   11
  XQ LOSS WILD-TYPE   45   48
         clus
vv        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ABSENT                9                45
  PRESENT              11                48
[1] 2 2
[1] FALSE
D80V31, continuous
D80V32, continuous
D80V33, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   13 13
  XQ LOSS WILD-TYPE 22 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13   13
  XQ LOSS WILD-TYPE   22   68
                                          clus
vv                                         XQ LOSS MUTATED XQ LOSS WILD-TYPE
  KERATINIZING SQUAMOUS CELL CARCINOMA                  13                22
  NON-KERATINIZING SQUAMOUS CELL CARCINOMA              13                68
[1] 2 2
[1] FALSE
D80V34, continuous
                   vv
clus                OTHER RADICAL HYSTERECTOMY SIMPLE HYSTERECTOMY
  XQ LOSS MUTATED       1                   22                   0
  XQ LOSS WILD-TYPE     2                   91                   5
D80V35, multiclass
                      clus
vv                     XQ LOSS MUTATED XQ LOSS WILD-TYPE
  OTHER                              1                 2
  RADICAL HYSTERECTOMY              22                91
  SIMPLE HYSTERECTOMY                0                 5
[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"
                   vv
clus                CURRENT USER FORMER USER NEVER USED
  XQ LOSS MUTATED              2           7         11
  XQ LOSS WILD-TYPE            6          33         29
D80V36, multiclass
              clus
vv             XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CURRENT USER               2                 6
  FORMER USER                7                33
  NEVER USED                11                29
[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, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   15  1
  XQ LOSS WILD-TYPE 58 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     15    1
  XQ LOSS WILD-TYPE   58   13
         clus
vv        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ABSENT               15                58
  PRESENT               1                13
[1] 2 2
[1] FALSE
D80V39, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                 8 
       TCGA-C5-A1BN        TCGA-C5-A1MH        TCGA-C5-A1MP        TCGA-EK-A2RO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HM-A3JK        TCGA-JW-A852        TCGA-MU-A51Y        TCGA-MU-A8JM 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
                   vv
clus                T1A T1A1 T1B T1B1 T1B2 T2 T2A T2A1 T2A2 T2B T3B T4 TX
  XQ LOSS MUTATED     1    0   4   10    7  0   1    0    3   1   0  0  0
  XQ LOSS WILD-TYPE   1    1  18   41   14  3   5    6    5  12   2  1  7
D80V40, multiclass
      clus
vv     XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1A                1                 1
  T1A1               0                 1
  T1B                4                18
  T1B1              10                41
  T1B2               7                14
  T2                 0                 3
  T2A                1                 5
  T2A1               0                 6
  T2A2               3                 5
  T2B                1                12
  T3B                0                 2
  T4                 0                 1
  TX                 0                 7
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V41, continuous
